Re: [Freesurfer] mri_vol2surf, error: mghRead(/mri/orig.mgz, -1)

[Douglas N. Greve]

Can you confirm that /subjects/CI_01/mri/orig.mgz exists? Usually, your  
SUBJECTS_DIR would not be directly in root, especially on a mac, but it 
is not impossible.


On 10/14/2022 7:17 AM, Wandschneider, Britta wrote:


External Email - Use Caution

Hello,

I am trying to map tumour+oedema lesion masks (generated with ITKSnap) 
to subjects' freesurfer surface (in native space) using mri_vol2surf.


This is an example of the command I am using for a specific subject:

mri_vol2surf --mov CI_01_t+oedema_corrected.nii\

--fwhm 0 \

--regheader CI_01 \

--hemi lh --surf pial \

--projdist-max 0 1 0.1 \

--interp trilinear\

--surfreg sphere.reg \

--icoorder 5 \

--out CI_01_t+oedema_corrected_lh.mgh


However, I get this error message:


IcoOrder = 5, nIcoVtxs = 10242

srcvol = CI_01_t+oedema_corrected.nii

srcreg unspecified

srcregold = 0

srcwarp unspecified

surf = pial

hemi = lh

ProjDist = 0.5

reshape = 0

interp = trilinear

float2int = round

GetProjMax = 1

INFO: float2int code = 0

INFO: this is an unsiged short. I'll try to read it, but

it might not work if there are values over 32k

INFO: using NIfTI-1 qform

INFO: changing type to float

Done loading volume

Computing registration from header.

Using /subjects/CI_01/mri/orig.mgz as target reference.

error: mghRead(/subjects/CI_01/mri/orig.mgz, -1): could not open file

klp32e:7.1.1 Britta$



I have tried the same command with a different freesurfer version 
(6.0.0), which lead to the same problem. The /mri/orig.mgz loads in 
freeview and looks fine to me. I searched the mailing list but have 
not found a post with this error being reported.


I am using version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551
on MacOS Mojave version 10.14.6

I would be very grateful for any advice.

Best wishes
Britta



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Re: [Freesurfer] mri_vol2surf error

[Douglas N. Greve]

Pick a hemisphere (either lh or rh). Also, you should verify that your 
volume overlays on fsaverage correctly with something like
tkmeditfv fsaverage orig.mgz -surfs -fminmax .01 1 -ov 
rReslice_Combined_roi_meanRD.nii  -reg 
$FREESURFER_HOME/average/mni152.register.dat




On 7/11/2022 6:23 PM, Rachel Wagner wrote:


External Email - Use Caution

Hello everyone,

I am trying to display my lesion map I created in Matlab on a cortical 
surface, and am getting the following error:


developer@developer-VirtualBox:~$ mri_vol2surf --mov 
rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject fsaverage 
--hemi lhrh --out lh_spm.mgh --projfrac-max 0 1 .1


srcvol = rReslice_Combined_roi_meanRD.nii

srcreg = /usr/local/freesurfer/7.2.0/average/mni152.register.dat

srcregold = 0

srcwarp unspecified

surf = white

hemi = lhrh

trgsubject = fsaverage

surfreg = sphere.reg

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 1

INFO: float2int code = 0

Done loading volume

INFO: This REGISTER_DAT transform is valid only for volumes between  
COR types with c_(r,a,s) = 0.


Input reg is register.dat

 original matrix ---

0.99753  -0.00732   0.01760   0.95709;

-0.01296  -0.00926   0.99706  -17.81596;

-0.01460  -1.00094   0.00244  -18.54964;

0.0   0.0   0.0   1.0;

 original matrix ---

Reading surface /usr/home//fsaverage/surf/lhrh.white

error: No such file or directory

error: MRISread(/usr/home//fsaverage/surf/lhrh.white): could not open file

error: No such file or directory

error: mri_vol2surf: could not read surface 
/usr/home//fsaverage/surf/lhrh.white


Could anyone help me fix this? I am very new to this software and need 
to have this results ready for my supervisor if possible!


Thank you,

Rachel


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Re: [Freesurfer] mri_vol2surf clarification

[Douglas N. Greve]

Sorry, I don't understand what you are trying to do. Extract ROI (eg, 
hippocampal) time courses?


On 9/14/2021 4:29 AM, Alice Giubergia wrote:


External Email - Use Caution

Dear Freesurfer's experts,
I am dealing with time course extraction from preprocessed 
(prerpoc-sess) task functional data; I was able to extract the time 
courses from the fsaverage sampled surfaces 
fmcpr.up.sm3.fsaverage.lh.nii.gz thanks to mri_segstats, but I was 
wondering how to handle the data sampled to the MNI space 
fmcpr.up.sm5.mni305.2mm.nii.gz. I think I should run mri_vol2surf to 
get a surface but I don't get the kind of registration option should I 
use.

mri_vol2surf --src fmcpr.up.sm5.mni305.2mm.nii.gz
I would appreciate any suggestion,
many thanks,
Alice

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Re: [Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

[Douglas N. Greve]

Yes, 2x the thickness

On 3/10/2021 11:17 PM, Horn, Mitchell Jacob wrote:


Dear FS Experts,

When using --projfrac-max or --projfrac-avg, how is the “min” 
component defined? If I specify:


--projfrac-max -2 1 0.1

Is the min (-2) simply 2x the thickness at each vertex below/inside 
the GM/WM boundary?


Thanks in advance!

Mitch


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Re: [Freesurfer] mri_vol2surf resolution warning

[Douglas N. Greve]

That registration assume that the input is the MNI152 volume with 1mm 
voxel size. This still might work, but I would check the registration 
between the 1mm MNI152 and the 6mm volume


On 2/26/2021 12:35 PM, Russo, Andrew William wrote:

Hello,

I am moving a 6mm volume from MNI152 to fsaverage for group analysis 
and I get the following warning:


mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg 
--hemi lh --interp nearest --surf-fwhm 4


WARNING: the voxel resolution in the source volume (6,6,6) differs 
from that listed in the registration file (1,1,1)


Do you know if this needs to be corrected or if there is a better method?

Thanks for the help,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531

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Re: [Freesurfer] mri_vol2surf MRISread error

[Douglas N. Greve]

Does that file exist?
What is your $SUBJECTS_DIR?
Can you send the full terminal output?

On 10/4/2020 2:05 AM, KN Qiao wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
mri_vol2surf --mov $mask_dir/rest_brainmask.nii.gz --reg 
$reg_dir/rest2t1.dat --trgsubject fsaverage --interp trilin --projfrac 
0.5 --hemi ${hemi} --o ${mask_dir}/mask.fsaverage.${hemi}.nii.gz 
--noreshape --cortex --surfreg sphere.reg

Error:
Loading label 
/Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label

Reading surface /Applications/freesurfer/subjects/freesurfer/surf/lh.white
MRISread(/Applications/freesurfer/subjects/freesurfer/surf/lh.white): 
could not open file

No such file or directory
This problem happens again when I try to use this command on a server 
in my lab.
I didn’t get why it attempted to get surface from 
/Applications/freesurfer/subjects/freesurfer
Should it try /Applications/freesurfer/subjects/fsaverage as well? It 
can load label properly.

Freesurfer version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: Darwin-OSX and CentOS6_x86_64

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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Also I missed that you upsampled the volume fMRI file massively as well.  
Indeed, this is not how I would recommend going about things, particularly in a 
memory limited environment.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 1:11 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subj

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Mason Wells]

External Email - Use Caution

Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any una

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] mri_vol2surf

[Douglas N. Greve]

Try this version (for linux)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf
If you run it without any arguments, it will print help. At the very end 
you will see a flag called --vol2surf



On 5/30/2020 11:08 AM, Nasr, Shahin,Ph.D. wrote:

Hi Surfers,
    Is there anyway to pass the full address of a surface to 
mri_vol2surf? To clarify, we are using surfaces that are saved outside 
/surf/ and we prefer not to relocate them every time that we want 
to use mri_vol2surf.


Thanks

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Re: [Freesurfer] mri_vol2surf projections for subcortical structures

[Bruce Fischl]

Hi Niels

I don't see why not. vol2surf takes the surface location and the surface 
normal and sampled from the volume onto the surface using those two pieces 
of local information. Global surface topology shouldn't matter

cheers
Bruce

On Sun, 
29 Mar 2020, Niels Janssen . wrote:




External Email - Use Caution

Dear list

I am working on a project in which we want to extract hippocampal surfaces
using mri_tessellate and then overlay these surfaces with fmri activations
from nifti files using mri_vol2surf. However, I am unclear whether
mri_vol2surf can be used for surfaces derived from subcortical structures
like the hippocampus. Crucially, these structures are unlike the cortex in
that they have a closed shape and therefore the projection of activation to
a surface may be more complex than in the case of cortex (which surface
normal should one take?). So I guess my question is whether mri_vol2surf
works for these kinds of surfaces or whether some other approach should be
used. Thanks!

Niels

--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/

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Re: [Freesurfer] mri_vol2surf produces invalid surface

[Shuntaro Aoki]

External Email - Use Caution

Thanks a lot.
Now I understand what was wrong and resolve it.


Shuntaro

2020年2月29日(土) 6:20 Douglas N. Greve :
>
> mri_vol2surf does not actually produce a surface, it produces a surface
> overlay (ie, a value for each vertex). You can to run recon-all to
> produce a surface
>
> On 2/27/2020 4:49 AM, Shuntaro Aoki wrote:
> >  External Email - Use Caution
> >
> > Dear mailing list,
> >
> > I was trying to convert a volume image to a freesurfer surface (as
> > gii) with `mri_vol2surf` for visualization, but ended up with invalid
> > surface data (i.e., a file not loadable by freeview).
> >
> > What I did was:
> >
> > ---
> > % mri_vol2surf --version
> > stable5
> > % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub
> > --hemi lh --out ./sample_vol2surf_lh.gii
> > ---
> >
> > Here, `sample_volume.nii.gz` is a volume image (such as a statistical
> > map) registered to an individual reference T1w image of subject
> > `sample-sub`, which was the input of recon-all for the subject.
> > The command completed without errors:
> >
> > ---
> > srcvol = ./sample_volume.nii.gz
> > srcreg unspecified
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Computing registration from header.
> >Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz
> > as target reference.
> > Reading surface
> > /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white
> > Done reading source surface
> > Mapping Source Volume onto Source Subject Surface
> >   1 0 0 0
> > using old
> > Done mapping volume to surface
> > Number of source voxels hit = 31055
> > Writing to ./sample_vol2surf_lh.gii
> > Dim: 155685 1 1
> > ---
> >
> > Then I tried to open the resulting surface `sample_vol2surf_lh.gii`
> > with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed
> > to load Surface".
> > I also got the following shell output:
> >
> > ---
> > mriseadGIFTIfile: mris is NULL! found when parsing file
> > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> > MRISread failed
> > mriseadGIFTIfile: mris is NULL! found when parsing file
> > /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> > ---
> >
> > The output of `mris_info` is:
> >
> > ---
> > % mris_info sample_vol2surf_lh.gii
> > ==
> > gifti_image struct
> >  version= 1.0
> >  numDA  = 1
> > gim->meta nvpairs struct, len = 3 :
> >  nvpair: 'UserName' = 'aoki'
> >  nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020'
> >  nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 
> > 2010'
> >
> > gim->labeltable giiLabelTable struct, len = 0 :
> > --
> > gim->darray[0] giiDataArray struct
> >  intent  0 = NIFTI_INTENT_NONE
> >  datatype   16 = NIFTI_TYPE_FLOAT32
> >  ind_ord 1 = RowMajorOrder
> >  num_dim   = 1
> >  dims  = 155685, 0, 0, 0, 0, 0
> >  encoding3 = GZipBase64Binary
> >  endian  2 = LittleEndian
> >  ext_fname =
> >  ext_offset= 0
> > darray->meta nvpairs struct, len = 0 :
> >  data   = 
> >  nvals  = 155685
> >  nbyper = 4
> >  numCS  = 0
> > darray->ex_atrs nvpairs struct, len = 0 :
> > --
> > gifti_image struct
> >  swapped= 0
> >  compressed = 1
> >   -- darray totals: 1 MB
> > gim->ex_atrs nvpairs struct, len = 0 :
> > ==
> > ---
> >
> > I checked matching between voxels in the input volume and the surface
> > with the output of --srchit option and found the registration was
> > fine.
> >
> > I also tried mgh output but got another invalid file.
> >
> > ---
> > % mris_info sample_vol2surf_lh.mgh
> > ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices!
> > Probably trying to use a scalar data file as a surface!
> >
> > No such file or directory
> > ---
> >
> > I would appreciate any advice on this.
> >
> > Regards,
> >
> >
> > Shuntaro
> >
> >
>
> ___
> Freesurfer mailing list
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-- 

Shuntaro C. Aoki, Ph.D.

Program-specific Researcher
Neuroinformatics group
Graduate School of Informatics
Kyoto University

s_a...@i.kyoto-u.ac.jp


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Re: [Freesurfer] mri_vol2surf produces invalid surface

[Douglas N. Greve]

mri_vol2surf does not actually produce a surface, it produces a surface 
overlay (ie, a value for each vertex). You can to run recon-all to 
produce a surface

On 2/27/2020 4:49 AM, Shuntaro Aoki wrote:
>  External Email - Use Caution
>
> Dear mailing list,
>
> I was trying to convert a volume image to a freesurfer surface (as
> gii) with `mri_vol2surf` for visualization, but ended up with invalid
> surface data (i.e., a file not loadable by freeview).
>
> What I did was:
>
> ---
> % mri_vol2surf --version
> stable5
> % mri_vol2surf --src ./sample_volume.nii.gz --regheader sample-sub
> --hemi lh --out ./sample_vol2surf_lh.gii
> ---
>
> Here, `sample_volume.nii.gz` is a volume image (such as a statistical
> map) registered to an individual reference T1w image of subject
> `sample-sub`, which was the input of recon-all for the subject.
> The command completed without errors:
>
> ---
> srcvol = ./sample_volume.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>Using /home/share/data/fmri/freesurfer/subjects/sample-sub/mri/orig.mgz
> as target reference.
> Reading surface
> /home/share/data/fmri/freesurfer/subjects/sample-sub/surf/lh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>   1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 31055
> Writing to ./sample_vol2surf_lh.gii
> Dim: 155685 1 1
> ---
>
> Then I tried to open the resulting surface `sample_vol2surf_lh.gii`
> with freeview (ver 1.0 build 2013-05-13) but it failed, saying "Failed
> to load Surface".
> I also got the following shell output:
>
> ---
> mriseadGIFTIfile: mris is NULL! found when parsing file
> /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> MRISread failed
> mriseadGIFTIfile: mris is NULL! found when parsing file
> /home/mu/aoki/work/surf_sphere/sample_vol2surf_lh.gii
> ---
>
> The output of `mris_info` is:
>
> ---
> % mris_info sample_vol2surf_lh.gii
> ==
> gifti_image struct
>  version= 1.0
>  numDA  = 1
> gim->meta nvpairs struct, len = 3 :
>  nvpair: 'UserName' = 'aoki'
>  nvpair: 'Date' = 'Thu Feb 27 17:32:40 2020'
>  nvpair: 'gifticlib-version' = 'gifti library version 1.09, 28 June, 2010'
>
> gim->labeltable giiLabelTable struct, len = 0 :
> --
> gim->darray[0] giiDataArray struct
>  intent  0 = NIFTI_INTENT_NONE
>  datatype   16 = NIFTI_TYPE_FLOAT32
>  ind_ord 1 = RowMajorOrder
>  num_dim   = 1
>  dims  = 155685, 0, 0, 0, 0, 0
>  encoding3 = GZipBase64Binary
>  endian  2 = LittleEndian
>  ext_fname =
>  ext_offset= 0
> darray->meta nvpairs struct, len = 0 :
>  data   = 
>  nvals  = 155685
>  nbyper = 4
>  numCS  = 0
> darray->ex_atrs nvpairs struct, len = 0 :
> --
> gifti_image struct
>  swapped= 0
>  compressed = 1
>   -- darray totals: 1 MB
> gim->ex_atrs nvpairs struct, len = 0 :
> ==
> ---
>
> I checked matching between voxels in the input volume and the surface
> with the output of --srchit option and found the registration was
> fine.
>
> I also tried mgh output but got another invalid file.
>
> ---
> % mris_info sample_vol2surf_lh.mgh
> ERROR: MRISread: file 'sample_vol2surf_lh.mgh' has 0 vertices!
> Probably trying to use a scalar data file as a surface!
>
> No such file or directory
> ---
>
> I would appreciate any advice on this.
>
> Regards,
>
>
> Shuntaro
>
>

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Re: [Freesurfer] mri_vol2surf fails

[Greve, Douglas N.,Ph.D.]

Are those values actually 0 or just very small? Is that area dark on the 
T2*?

On 8/26/19 11:20 AM, Sackl, Maximilian wrote:
>  External Email - Use Caution
>
> Thank you for the prompt answer!
>
> No, the T2* map within the pial and WM does include values ...
> Any ideas?
>
> On 26.08.2019 16:59, Greve, Douglas N.,Ph.D. wrote:
>> You should bring up the T2* with the surfaces. Is it possible that the
>> T2* just did not include that particular bit?
>>
>> On 8/26/19 10:38 AM, Sackl, Maximilian wrote:
>>>External Email - Use Caution
>>>
>>> Dear FreeSurfer experts,
>>>
>>> I was trying to perform a GLM fit with T2* data, projected on the
>>> cortical surface.
>>>
>>> For the preparation of the 4D-input file (needed for mri_preproc) I used
>>> the mri_vol2surf command and encountered the following problem. There
>>> appear regions without any values, (screenshot mri_vol2surf_output.png),
>>> although the segmentation of the pial and WM surface seem to be correct.
>>> (screenshot pialSurface.png).
>>>
>>> Do you have any idea, how to solve this problem?
>>>
>>>
>>> Thank you very much!
>>>
>>> Best regards,
>>> Maximilian
>>>
>>>
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Re: [Freesurfer] mri_vol2surf fails

[Greve, Douglas N.,Ph.D.]

You should bring up the T2* with the surfaces. Is it possible that the 
T2* just did not include that particular bit?

On 8/26/19 10:38 AM, Sackl, Maximilian wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I was trying to perform a GLM fit with T2* data, projected on the
> cortical surface.
>
> For the preparation of the 4D-input file (needed for mri_preproc) I used
> the mri_vol2surf command and encountered the following problem. There
> appear regions without any values, (screenshot mri_vol2surf_output.png),
> although the segmentation of the pial and WM surface seem to be correct.
> (screenshot pialSurface.png).
>
> Do you have any idea, how to solve this problem?
>
>
> Thank you very much!
>
> Best regards,
> Maximilian
>
>
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Re: [Freesurfer] mri_vol2surf error

[Greve, Douglas N.,Ph.D.]

Not ssure what is happening. CAn you send the full terminal output. 
Also, remove the --out_type flag. No need to include --surfreg 
sphere.reg (but should not hurt anything).

On 8/14/19 12:37 PM, Pratik Kashyap wrote:
>
> External Email - Use Caution
>
> mri_vol2surf --cortex --hemi lh --interp trilinear --o rest2.nii.gz 
> --out_type niigz --reg register.dat --projfrac-avg 0.500 --mov 
> rest2.nii --surfreg sphere.reg --trgsubject fsaverage
>
>
> A source volume path must be supplied
>
>
> Hey,
>
>
> I'm running the above command, getting an error 'A source volume path 
> must be specified'
>
> I checked all the source paths, they exist. But the output path 
> doesn't , which is weird as it isn't a source path.
>
>
> Please help,
>
> PK
>
>
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Re: [Freesurfer] mri_vol2surf for functional 4D BOLD data only mapping 1 frame

[Greve, Douglas N.,Ph.D.]

did you check the output? I think it should have the appropriate number of 
frames. You can use mri_info to check the dimensions

On 5/13/2019 7:35 AM, Robert Austin Bruce Benn wrote:

External Email - Use Caution

Hi There,

I’m currently trying to run mri_vol2surf on some animal data and surfaces I’ve 
been working with.
I’m having a bit of a problem with the command mri_vol2surf.
I seem to be able to project my functional volume to my surface, however I’m 
currently only projecting the first volume of my functional time series onto 
the surface.
I realize the default option for frame is the first volume if output is set to 
a paint file, however I’m not trying to do that.

Ideally I’d like to project all the volumes for later connectivity analysis.

The command and terminal output are as  follows:

mri_vol2surf --mov rest.acp/filtered_func_data_clean.nii.gz --reg 
rest.acp/reg/example_func2FS.dat --surf white  --projfrac 0.5 --hemi lh --o 
rest.acp/test.func.mgh

srcvol = rest.acp/filtered_func_data_clean.nii.gz
srcreg = rest.acp/reg/example_func2FS.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
INFO: This REGISTER_DAT transform is valid only for volumes between  COR types 
with c_(r,a,s) = 0.
Input reg is register.dat
 original matrix ---
 0.99985  -0.01410   0.01053   2.56773;
 0.01269   0.99230   0.12321  -20.18632;
-0.01219  -0.12306   0.99232   0.65897;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface /Volumes/brain/PCP_func/5489/anat/surf/lh.white
Done reading source surface
Reading thickness /Volumes/brain/PCP_func/5489/anat/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 2868
Writing to rest.acp/test.func.nii
Dim: 19181 1 1

The actual functional volumes has 300 volumes, so I feel like I should be 
getting Dim: 19181 1 1 300 ?

any advice?

thanks,

austin



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Re: [Freesurfer] mri_vol2surf error

[Loïc Daumail]

External Email - Use Caution

Dear Doug Greve,

Sorry, issue solved!
I had used a wrong path directory in the commandline... it’s now working
perfectly well.
Thanks for your help,

Sincerely,

Loïc Daumail

Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> can you send the full terminal output of the mri_surf2vol command?
>
> On 4/17/19 5:59 AM, Loïc Daumail wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > I am currently trying to use mri_vol2surf on my bold data. I typed
> > this commandline :
> > "
> > mri_vol2surf --mov
> >
> ${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>
> > \
> >   --mni152reg \
> >   --projfrac-avg 0.2 0.8 0.1 \
> >   --trgsubject fsaverage5 \
> >   --interp nearest \
> >   --hemi ${hemi} \
> >   --surf-fwhm 6.0 --cortex --noreshape \
> >   --o ${dir1}/${subject}/${subject}${scan}.fsa5.${hemi}.mgz
> > "
> >
> > However, when trying to run it, I obtain the following error: ERROR:
> > could not read .. as type 24
> > detail:
> > "
> > srcvol =
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> > srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > trgsubject = fsaverage5
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > niiRead(): error opening file
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> > ERROR: could not read
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>
> > as type 24
> > "
> > but when converting from nii.gz to mgz, I obtain the following :
> > "
> > mri_convert
> >
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
>
> >
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from
> >
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz...
> > niiRead(): error opening file
> >
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> > srcvol =
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
> > srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > trgsubject = fsaverage5
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> >
> mghRead(/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz,
>
> > -1): could not open file
> > ERROR: could not read
> >
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
>
> > as type 3
> > "
> >
> > I also copied the output from mri_info on my bold image in .nii.gz
> format:
> > "
> > mri_info
> >
> sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> > Volume information for
> >
> sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> >   type: nii
> > dimensions: 91 x 109 x 91 x 200
> >voxel sizes: 2., 2., 2.
> >   type: FLOAT (3)
> >fov: 182.000
> >dof: 0
> > xstart: -91.0, xend: 91.0
> > ystart: -109.0, yend: 109.0
> > zstart: -91.0, zend: 91.0
> > TR: 3220.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> > angle: 0.00 degrees
> >nframes: 200
> >PhEncDir: UNKNOWN
> > ras xform present
> > xform info: x_r =   1., y_r =   0., z_r =   0., c_r
> > = 0.5000
> >   : x_a =   0., y_a =   1., z_a =   0., c_a
> > =   -17.5000
> >   : x_s =   0., y_s =   0., z_s =   1., c_s
> > =18.5000
> > Orientation   : RAS
> > Primary Slice Direction: axial
> >
> > voxel to ras transform:
> > 2.   0.   0.   

Re: [Freesurfer] mri_vol2surf error

[Greve, Douglas N.,Ph.D.]

can you send the full terminal output of the mri_surf2vol command?

On 4/17/19 5:59 AM, Loïc Daumail wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am currently trying to use mri_vol2surf on my bold data. I typed 
> this commandline :
> "
> mri_vol2surf --mov 
> ${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>  
> \
>   --mni152reg \
>   --projfrac-avg 0.2 0.8 0.1 \
>   --trgsubject fsaverage5 \
>   --interp nearest \
>   --hemi ${hemi} \
>   --surf-fwhm 6.0 --cortex --noreshape \
>   --o ${dir1}/${subject}/${subject}${scan}.fsa5.${hemi}.mgz
> "
>
> However, when trying to run it, I obtain the following error: ERROR: 
> could not read .. as type 24
> detail:
> "
> srcvol = 
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> trgsubject = fsaverage5
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> niiRead(): error opening file 
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> ERROR: could not read 
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>  
> as type 24
> "
> but when converting from nii.gz to mgz, I obtain the following :
> "
> mri_convert 
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>  
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
>  
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz...
> niiRead(): error opening file 
> /mnt/data/loic2/embedding/recon_all_success/fmriprep/sub-002/func/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> srcvol = 
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
> srcreg = /home/loic.daumail/freesurfer/average/mni152.register.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> trgsubject = fsaverage5
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> mghRead(/mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz,
>  
> -1): could not open file
> ERROR: could not read 
> /mnt/data/loic2/embedding/vol2surf_derivatives/sub-002/sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.mgz
>  
> as type 3
> "
>
> I also copied the output from mri_info on my bold image in .nii.gz format:
> "
> mri_info 
> sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
> Volume information for 
> sub-002_ses-1_task-compassion_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
>   type: nii
>     dimensions: 91 x 109 x 91 x 200
>    voxel sizes: 2., 2., 2.
>   type: FLOAT (3)
>    fov: 182.000
>    dof: 0
>     xstart: -91.0, xend: 91.0
>     ystart: -109.0, yend: 109.0
>     zstart: -91.0, zend: 91.0
>     TR: 3220.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
> angle: 0.00 degrees
>    nframes: 200
>    PhEncDir: UNKNOWN
> ras xform present
>     xform info: x_r =   1., y_r =   0., z_r =   0., c_r 
> = 0.5000
>   : x_a =   0., y_a =   1., z_a =   0., c_a 
> =   -17.5000
>   : x_s =   0., y_s =   0., z_s =   1., c_s 
> =    18.5000
> Orientation   : RAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>     2.   0.   0.   -90.5000
>     0.   2.   0.  -126.5000
>     0.   0.   2.   -72.5000
>     0.   0.   0. 1.
>
> voxel-to-ras determinant 8
>
> ras to voxel transform:
>     0.5000  -0.  -0.    45.2500
>    -0.   0.5000  -0.    63.2500
>    -0.  -0.   0.5000    36.2500
>     0.   0.   0. 1.
> "
> Thanks in advance for your help,
>
> Sincerely,
>
> Loïc Daumail
> Université Lyon 1
>
> 

Re: [Freesurfer] mri_vol2surf sample inside and outside of pial

[Bruce Fischl]

yes, although note that neither one is guaranteed to be "inside" or 
"outside" at that distance (it might reenter the surface in the outwards 
normal direction, or leave the surface in the inwards direction)


cheers
Bruce
On Tue, 5 
Mar 2019, Michael Jordan wrote:




External Email - Use Caution

Hi,

I have a short question concerning the mri_vol2surf command.
Do the following parameters of the command return the maximum volume value (for 
each vertex) which
occurs between 10 mm outside and 10 mm inside the pial surface (along normal 
vector)?

 --projdist-max -10 10 0.25 --interp nearest --surf pial

Thank you very much!!

Regards Michael





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Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

[Bruce Fischl]

Hi Michael

you can use either --projfrac-avg or --projdist-avg (dist I guess if you 
want to specify 10mm). Note that this is an average along 1D (the surface 
normal direction), not in a volume window


cheers
Bruce
 On Wed, 27 Feb 2019, Michael 
Jordan wrote:




External Email - Use Caution

Hi Bruce,

thank you it worked!

Another short question:

I want mri_surf2vol to assign the average of all volume voxel values within 10 
mm to the
corresponding vertices.
So if there is only one voxel value greater than zero in the volume, all 
vertices which are closer
than 10 mm should
get that value (or the mean if there is more than one value). Can I use ' 
--projdist 10' for this
purpose?

Thank you!!

Cheers,
Michael

Am Mo., 18. Feb. 2019 um 15:01 Uhr schrieb Bruce Fischl 
:
  Hi Michael

  you can use --regheader, which uses the ras2vox matrices to compute the
  registration (which is also what freeview does).

  cheers
  Bruce
  On Mon, 18 Feb
  2019, Michael Jordan wrote:

  >
  > External Email - Use Caution
  >
  > Hi,
  >
  > i would like to sample the t-values of a SPM output volume 
(spmT_0001.nii) onto the
  pial surface of
  > the same subject.
  > The volume is already aligned to the surface files (so if I view the 
volume as well as
  the surface
  > files in Freeview they are already aligned).
  >
  > Therefore I am unsure how to use mri_vol2surf because from my point of 
view I do not
  need any
  > registration (srcreg).
  > Nevertheless the registration is required to run the command. I only 
found the
  --mni152reg option to
  > avoid specifying a registration.
  >
  > How I should use the mri_vol2surf command to sample the volume onto the 
pial surface
  of the same
  > subject under the condition that
  > surface and volume are already aligned?
  >
  > Thank you!
  >
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Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

[Michael Jordan]

External Email - Use Caution

Hi Bruce,

thank you it worked!

Another short question:

I want mri_surf2vol to assign the average of all volume voxel values within
10 mm to the corresponding vertices.
So if there is only one voxel value greater than zero in the volume, all
vertices which are closer than 10 mm should
get that value (or the mean if there is more than one value). Can I use '
--projdist 10' for this purpose?

Thank you!!

Cheers,
Michael

Am Mo., 18. Feb. 2019 um 15:01 Uhr schrieb Bruce Fischl <
fis...@nmr.mgh.harvard.edu>:

> Hi Michael
>
> you can use --regheader, which uses the ras2vox matrices to compute the
> registration (which is also what freeview does).
>
> cheers
> Bruce
> On Mon, 18 Feb
> 2019, Michael Jordan wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > i would like to sample the t-values of a SPM output volume
> (spmT_0001.nii) onto the pial surface of
> > the same subject.
> > The volume is already aligned to the surface files (so if I view the
> volume as well as the surface
> > files in Freeview they are already aligned).
> >
> > Therefore I am unsure how to use mri_vol2surf because from my point of
> view I do not need any
> > registration (srcreg).
> > Nevertheless the registration is required to run the command. I only
> found the --mni152reg option to
> > avoid specifying a registration.
> >
> > How I should use the mri_vol2surf command to sample the volume onto the
> pial surface of the same
> > subject under the condition that
> > surface and volume are already aligned?
> >
> > Thank you!
> >
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Re: [Freesurfer] mri_vol2surf for sampling spmT_0001.nii on pial surface

[Bruce Fischl]

Hi Michael

you can use --regheader, which uses the ras2vox matrices to compute the 
registration (which is also what freeview does).


cheers
Bruce
On Mon, 18 Feb 
2019, Michael Jordan wrote:




External Email - Use Caution

Hi,

i would like to sample the t-values of a SPM output volume (spmT_0001.nii) onto 
the pial surface of
the same subject.
The volume is already aligned to the surface files (so if I view the volume as 
well as the surface
files in Freeview they are already aligned).

Therefore I am unsure how to use mri_vol2surf because from my point of view I 
do not need any
registration (srcreg).
Nevertheless the registration is required to run the command. I only found the 
--mni152reg option to
avoid specifying a registration.

How I should use the mri_vol2surf command to sample the volume onto the pial 
surface of the same
subject under the condition that
surface and volume are already aligned?

Thank you!

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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[srishti goel]

External Email - Use Caution

Hello Bruce,

As suggested by you, I used tkmeditfv to view the volumetric maps on the
surface and it seems like the dACC cluster is lying outside the brain. I
checked the registration of the volumetric file using tkregisterfv but
surprisingly nothing shows up. I also tried using bbregister and then
checked the registration but the same thing happened, the volumetric map
doesn't show up in either of those cases.

I am confused, as to why that is happening and how can I fix it such that
all the clusters are appropriately aligned.

The files I am using have been exported from neuroelf program. I exported
them as analyze format (.img and .hdr) and then converted it to nifti
format using mri_convert. However, with both the analyze and nifti format,
similar things happened.

Any help is highly appreciated.

Thanks,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Tue, Jun 26, 2018 at 11:56 PM, Douglas Greve 
wrote:

> you can try
> tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3
> you may have to adjust the thresholds (fminmax)
>
>
> On 6/26/18 10:43 PM, srishti goel wrote:
>
> External Email - Use Caution
> Hello Bruce,
>
> You had mentioned about loading the volumetric maps with the surface to
> check that all my clusters are contained within the surfaces. Since I am
> very new to freesurfer, could you please guide to where I can find an
> appropriate command to do that.
>
> Thank you so much for all the help!
>
> Best,
> Srishti
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
> On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl  > wrote:
>
>> Hi Srishti
>>
>> you should be able to load the volumetric maps with the surfaces and make
>> sure that your clusters are contained within the surface.
>>
>> cheers
>> Bruce
>>
>> On Mon, 25 Jun 2018, srishti goel wrote:
>>
>>
>>> External Email - Use Caution
>>>
>>> They are separate clusters not the same clusters but we both of those
>>> don't show up when we
>>> project the volume maps on surface. Every other cluster comes up and
>>> this has happened in
>>> about 2-3 files. Are you absolutely sure that the surface in freesurfer
>>> includes dACC and
>>> insula?
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve 
>>> wrote:
>>>
>>>   It should be included. But dACC and insula are not close to each
>>> other. How can
>>>   there be a cluster that spans both?
>>>
>>>
>>>   On 6/23/18 7:54 PM, srishti goel wrote:
>>>
>>>   External Email - Use Caution
>>>
>>>   Hello,
>>> I am using mri_vol2surf to project my volume maps on to the surface.
>>> There is a
>>> dACC/insula cluster visible in my volume maps that doesn't show up when
>>> I project
>>> it on the surface.
>>>
>>> Is that because dACC/insula is not included in surfaces on Freesurfer?
>>>
>>> Thanks!
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> 

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[Douglas Greve]

you can try
tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3
you may have to adjust the thresholds (fminmax)

On 6/26/18 10:43 PM, srishti goel wrote:


External Email - Use Caution

Hello Bruce,

You had mentioned about loading the volumetric maps with the surface 
to check that all my clusters are contained within the surfaces. Since 
I am very new to freesurfer, could you please guide to where I can 
find an appropriate command to do that.


Thank you so much for all the help!

Best,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


Hi Srishti

you should be able to load the volumetric maps with the surfaces
and make sure that your clusters are contained within the surface.

cheers
Bruce

On Mon, 25 Jun 2018, srishti goel wrote:


External Email - Use Caution

They are separate clusters not the same clusters but we both
of those don't show up when we
project the volume maps on surface. Every other cluster comes
up and this has happened in
about 2-3 files. Are you absolutely sure that the surface in
freesurfer includes dACC and
insula?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

      It should be included. But dACC and insula are not close
to each other. How can
      there be a cluster that spans both?


      On 6/23/18 7:54 PM, srishti goel wrote:

      External Email - Use Caution

      Hello,
I am using mri_vol2surf to project my volume maps on to the
surface. There is a
dACC/insula cluster visible in my volume maps that doesn't
show up when I project
it on the surface.

Is that because dACC/insula is not included in surfaces on
Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12



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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[srishti goel]

External Email - Use Caution

Hello Bruce,

You had mentioned about loading the volumetric maps with the surface to
check that all my clusters are contained within the surfaces. Since I am
very new to freesurfer, could you please guide to where I can find an
appropriate command to do that.

Thank you so much for all the help!

Best,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl 
wrote:

> Hi Srishti
>
> you should be able to load the volumetric maps with the surfaces and make
> sure that your clusters are contained within the surface.
>
> cheers
> Bruce
>
> On Mon, 25 Jun 2018, srishti goel wrote:
>
>
>> External Email - Use Caution
>>
>> They are separate clusters not the same clusters but we both of those
>> don't show up when we
>> project the volume maps on surface. Every other cluster comes up and this
>> has happened in
>> about 2-3 files. Are you absolutely sure that the surface in freesurfer
>> includes dACC and
>> insula?
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve 
>> wrote:
>>
>>   It should be included. But dACC and insula are not close to each
>> other. How can
>>   there be a cluster that spans both?
>>
>>
>>   On 6/23/18 7:54 PM, srishti goel wrote:
>>
>>   External Email - Use Caution
>>
>>   Hello,
>> I am using mri_vol2surf to project my volume maps on to the surface.
>> There is a
>> dACC/insula cluster visible in my volume maps that doesn't show up when I
>> project
>> it on the surface.
>>
>> Is that because dACC/insula is not included in surfaces on Freesurfer?
>>
>> Thanks!
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[srishti goel]

External Email - Use Caution

Hi Bruce,

Thank you so much for your prompt help. Can I achieve that with:

tkregisterfv --mov [your volume maps] --regheader --s [the subject on whose
surface map is registered] --surfs --reg [file name]

Best,
Srishti

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl 
wrote:

> Hi Srishti
>
> you should be able to load the volumetric maps with the surfaces and make
> sure that your clusters are contained within the surface.
>
> cheers
> Bruce
>
> On Mon, 25 Jun 2018, srishti goel wrote:
>
>
>> External Email - Use Caution
>>
>> They are separate clusters not the same clusters but we both of those
>> don't show up when we
>> project the volume maps on surface. Every other cluster comes up and this
>> has happened in
>> about 2-3 files. Are you absolutely sure that the surface in freesurfer
>> includes dACC and
>> insula?
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve 
>> wrote:
>>
>>   It should be included. But dACC and insula are not close to each
>> other. How can
>>   there be a cluster that spans both?
>>
>>
>>   On 6/23/18 7:54 PM, srishti goel wrote:
>>
>>   External Email - Use Caution
>>
>>   Hello,
>> I am using mri_vol2surf to project my volume maps on to the surface.
>> There is a
>> dACC/insula cluster visible in my volume maps that doesn't show up when I
>> project
>> it on the surface.
>>
>> Is that because dACC/insula is not included in surfaces on Freesurfer?
>>
>> Thanks!
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>>
>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[Bruce Fischl]

Hi Srishti

you should be able to load the volumetric maps with the surfaces and make 
sure that your clusters are contained within the surface.


cheers
Bruce
On Mon, 25 Jun 
2018, srishti goel wrote:




External Email - Use Caution

They are separate clusters not the same clusters but we both of those don't 
show up when we
project the volume maps on surface. Every other cluster comes up and this has 
happened in
about 2-3 files. Are you absolutely sure that the surface in freesurfer 
includes dACC and
insula?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve  wrote:

  It should be included. But dACC and insula are not close to each other. 
How can
  there be a cluster that spans both?


  On 6/23/18 7:54 PM, srishti goel wrote:

  External Email - Use Caution

  Hello,
I am using mri_vol2surf to project my volume maps on to the surface. There is a
dACC/insula cluster visible in my volume maps that doesn't show up when I 
project
it on the surface.

Is that because dACC/insula is not included in surfaces on Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12



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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[srishti goel]

External Email - Use Caution

They are separate clusters not the same clusters but we both of those don't
show up when we project the volume maps on surface. Every other cluster
comes up and this has happened in about 2-3 files. Are you absolutely sure
that the surface in freesurfer includes dACC and insula?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve 
wrote:

> It should be included. But dACC and insula are not close to each other.
> How can there be a cluster that spans both?
>
> On 6/23/18 7:54 PM, srishti goel wrote:
>
> External Email - Use Caution
> Hello,
>
> I am using mri_vol2surf to project my volume maps on to the surface. There
> is a dACC/insula cluster visible in my volume maps that doesn't show up
> when I project it on the surface.
>
> Is that because dACC/insula is not included in surfaces on Freesurfer?
>
> Thanks!
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
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> is
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> contains patient information, please contact the Partners Compliance
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

[Douglas Greve]

It should be included. But dACC and insula are not close to each other. 
How can there be a cluster that spans both?



On 6/23/18 7:54 PM, srishti goel wrote:


External Email - Use Caution

Hello,

I am using mri_vol2surf to project my volume maps on to the surface. 
There is a dACC/insula cluster visible in my volume maps that doesn't 
show up when I project it on the surface.


Is that because dACC/insula is not included in surfaces on Freesurfer?

Thanks!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12



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Re: [Freesurfer] mri_vol2surf projection

[Douglas N. Greve]

You should first make sure that the registration is ok with

tkregister --mov ICA_split.nii.gz --regheader --s fsaverage5 --reg 
deleteme.dat

Note that going from a volume group space onto the surface is often not 
that good


On 06/11/2018 11:45 AM, Tom Vanasse wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I wanted to confirm that I properly performed the mri_vol2surf 
> command. I'm interested in projecting a z-score image (in Talairach 
> space) to an average surface (fsaverage5), using a mid-gray projection 
> fraction.
>
> mri_vol2surf --src ICA_split.nii.gz --regheader fsaverage5 --hemi 
> lh --o ICA_split_lh.nii --projfrac 0.5
>
> My --src volume has array size (80 x 96 x 70) with 2mm isotropic 
> voxels in Talairach space. The command ran without error, but I wanted 
> to be sure it is indeed the correct approach.
>
> Thanks,
>
> Tom Vanasse
>
> Thomas J. Vanasse
> Medical Physics PhD Candidate
> UT Health San Antonio
> Research Imaging Institute, Office 2.312
>
>
> ___
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf

[Martin Reuter]

Hi,Yes the longitudinal images after the long run are all aligned in the base space. You will find the map from each time point to the base in the base MRI transforms dir (maybe also in the long MRI transforms). Naming should make clear what reach one is.Best MartinAm 09.05.2018 21:11 schrieb "Douglas N. Greve" :There is a registration file that gets created by the longitudinal 

processing that can be used with mri_vol2vol. I don't know where the LTA 

file is, but maybe Martin can weigh in.





On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:

>

>

> Hi,

>

> I figured that part out: I can't load surfaces as volumes in freeview, 

> but rather i need to load them as an overlay to the subject white, or 

> pial surfaces.

>

> I have another question for which I can't find an answer to. After 

> registering myelin maps to the individual subjects, how do I 

> register/transform them into the subjects' longitudinal T1s (obtained 

> after the recon-all long command)?

>

> The broad goal that I am trying to achieve is longitudinal myelin 

> analysis. Any feedback is appreciated. Thanks!

>

> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 

> > wrote:

>

> I did: mri_vol2surf --src Myelin_conformed.mgz --out

> C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5

>

> Now I'm just getting the error "freadFloat: fread failed" a whole

> bunch of times and the terminal gets stuck. Any suggestions?

>

> I checked Myelin_conformed.mgz and loaded it with orig.mgz in

> freeview and they look fine with great overlap and registration

>

> Thanks!

>

> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve

> > wrote:

>

> Specify a file format for the output (eg, C01.mgz)

>

>

> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:

>>

>>

>> Hi,

>>

>> Thank you for the prompt response.

>>

>> I used the following command:

>>

>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after

>> mri_vol2vol from the previous step) --out C01 --regheader C01

>> --hemi lh --projfrac 0.5

>>

>> This created two files called COR-.info and COR001. I tried

>> loaded the COR001 file into freeview and tksurfer, but I keep

>> the error "MRISalloc(8229512, 76): could allocated faces \

>> cannot allocate memory

>>

>> Am I making a mistake somewhere?

>>

>> Thanks,

>>

>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve

>> > wrote:

>>

>> That all looks correct. For the registration, just use

>> --regheader C01

>>

>>

>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:

>>>

>>>

>>> Hi,

>>>

>>> It's my first time using FreeSurfer and I'd like some

>>> guidance regarding some of my steps.

>>>

>>> I'm attempting to perform myelin mapping as outlined in

>>> the paper by Righart (2017) Ann Neurol. Overall, I want

>>> to calculate myelin maps from each subject, sample them

>>> from the mid-cortical level to create cortical myelin

>>> surface maps, and perform vertexwise and ROI based analyses.

>>>

>>> Here's what I've done so far:

>>>

>>> 1. recon-all for all the subjects

>>> 2. Used bbregister to register the native T2 scans to

>>> the conformed T1 scans using this command: bbregister

>>> --s C01 --mov C01_T2.nii --init-fsl --reg register.dat

>>> --t2 (my understanding here is that this generates the

>>> .dat file that has the transformation to register the T2

>>> image to the conformed orig.mgz file from subject C01)

>>> 3. Applied the register.dat file to the native T2 using

>>> mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz

>>> --fstarg --reg register.dat (this registers the T2 to

>>> the orig.mgz file in the conformed space)

>>>

>>> The next step for me is to perform mri_vol2surf. My

>>> question here is, which file should I select for the

>>> --srcreg flag and what should the --trgsubject input be?

>>> Secondly, am I on the right track to complete the

>>> analysis i.e., correct file types and my understanding

>>> of the steps? Clarifications regarding these questions

>>> and any suggestions for further directions will be very

>>> helpful!

>>>

>>> Let me know. Thanks!

>>>

>>>

>>> ___

>>> Freesurfer mailing list

>>> Freesurfer@nmr.mgh.harvard.edu

>>> 

Re: [Freesurfer] mri_vol2surf

[Douglas N. Greve]

There is a registration file that gets created by the longitudinal 
processing that can be used with mri_vol2vol. I don't know where the LTA 
file is, but maybe Martin can weigh in.


On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:
>
>
> Hi,
>
> I figured that part out: I can't load surfaces as volumes in freeview, 
> but rather i need to load them as an overlay to the subject white, or 
> pial surfaces.
>
> I have another question for which I can't find an answer to. After 
> registering myelin maps to the individual subjects, how do I 
> register/transform them into the subjects' longitudinal T1s (obtained 
> after the recon-all long command)?
>
> The broad goal that I am trying to achieve is longitudinal myelin 
> analysis. Any feedback is appreciated. Thanks!
>
> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 
> > wrote:
>
> I did: mri_vol2surf --src Myelin_conformed.mgz --out
> C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5
>
> Now I'm just getting the error "freadFloat: fread failed" a whole
> bunch of times and the terminal gets stuck. Any suggestions?
>
> I checked Myelin_conformed.mgz and loaded it with orig.mgz in
> freeview and they look fine with great overlap and registration
>
> Thanks!
>
> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve
> > wrote:
>
> Specify a file format for the output (eg, C01.mgz)
>
>
> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
>>
>>
>> Hi,
>>
>> Thank you for the prompt response.
>>
>> I used the following command:
>>
>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after
>> mri_vol2vol from the previous step) --out C01 --regheader C01
>> --hemi lh --projfrac 0.5
>>
>> This created two files called COR-.info and COR001. I tried
>> loaded the COR001 file into freeview and tksurfer, but I keep
>> the error "MRISalloc(8229512, 76): could allocated faces \
>> cannot allocate memory
>>
>> Am I making a mistake somewhere?
>>
>> Thanks,
>>
>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve
>> > wrote:
>>
>> That all looks correct. For the registration, just use
>> --regheader C01
>>
>>
>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>>>
>>>
>>> Hi,
>>>
>>> It's my first time using FreeSurfer and I'd like some
>>> guidance regarding some of my steps.
>>>
>>> I'm attempting to perform myelin mapping as outlined in
>>> the paper by Righart (2017) Ann Neurol. Overall, I want
>>> to calculate myelin maps from each subject, sample them
>>> from the mid-cortical level to create cortical myelin
>>> surface maps, and perform vertexwise and ROI based analyses.
>>>
>>> Here's what I've done so far:
>>>
>>> 1. recon-all for all the subjects
>>> 2. Used bbregister to register the native T2 scans to
>>> the conformed T1 scans using this command: bbregister
>>> --s C01 --mov C01_T2.nii --init-fsl --reg register.dat
>>> --t2 (my understanding here is that this generates the
>>> .dat file that has the transformation to register the T2
>>> image to the conformed orig.mgz file from subject C01)
>>> 3. Applied the register.dat file to the native T2 using
>>> mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz
>>> --fstarg --reg register.dat (this registers the T2 to
>>> the orig.mgz file in the conformed space)
>>>
>>> The next step for me is to perform mri_vol2surf. My
>>> question here is, which file should I select for the
>>> --srcreg flag and what should the --trgsubject input be?
>>> Secondly, am I on the right track to complete the
>>> analysis i.e., correct file types and my understanding
>>> of the steps? Clarifications regarding these questions
>>> and any suggestions for further directions will be very
>>> helpful!
>>>
>>> Let me know. Thanks!
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> 

Re: [Freesurfer] mri_vol2surf

[Abdullah Ishaque]

External Email - Use Caution

Hi,

I figured that part out: I can't load surfaces as volumes in freeview, but
rather i need to load them as an overlay to the subject white, or pial
surfaces.

I have another question for which I can't find an answer to. After
registering myelin maps to the individual subjects, how do I
register/transform them into the subjects' longitudinal T1s (obtained after
the recon-all long command)?

The broad goal that I am trying to achieve is longitudinal myelin analysis.
Any feedback is appreciated. Thanks!

On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque 
wrote:

> I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz
> --regheader C01 --hemi lh --projfrac 0.5
>
> Now I'm just getting the error "freadFloat: fread failed" a whole bunch of
> times and the terminal gets stuck. Any suggestions?
>
> I checked Myelin_conformed.mgz and loaded it with orig.mgz in freeview and
> they look fine with great overlap and registration
>
> Thanks!
>
> On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve 
> wrote:
>
>> Specify a file format for the output (eg, C01.mgz)
>>
>> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
>>
>> External Email - Use Caution
>> Hi,
>>
>> Thank you for the prompt response.
>>
>> I used the following command:
>>
>> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol
>> from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
>>
>> This created two files called COR-.info and COR001. I tried loaded the
>> COR001 file into freeview and tksurfer, but I keep the error
>> "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
>>
>> Am I making a mistake somewhere?
>>
>> Thanks,
>>
>> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve 
>> wrote:
>>
>>> That all looks correct. For the registration, just use --regheader C01
>>>
>>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>>>
>>>
>>> Hi,
>>>
>>> It's my first time using FreeSurfer and I'd like some guidance regarding
>>> some of my steps.
>>>
>>> I'm attempting to perform myelin mapping as outlined in the paper by
>>> Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from
>>> each subject, sample them from the mid-cortical level to create cortical
>>> myelin surface maps, and perform vertexwise and ROI based analyses.
>>>
>>> Here's what I've done so far:
>>>
>>> 1. recon-all for all the subjects
>>> 2. Used bbregister to register the native T2 scans to the conformed T1
>>> scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl
>>> --reg register.dat --t2 (my understanding here is that this generates the
>>> .dat file that has the transformation to register the T2 image to the
>>> conformed orig.mgz file from subject C01)
>>> 3. Applied the register.dat file to the native T2 using mri_vol2vol
>>> --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this
>>> registers the T2 to the orig.mgz file in the conformed space)
>>>
>>> The next step for me is to perform mri_vol2surf. My question here is,
>>> which file should I select for the --srcreg flag and what should the
>>> --trgsubject input be? Secondly, am I on the right track to complete the
>>> analysis i.e., correct file types and my understanding of the steps?
>>> Clarifications regarding these questions and any suggestions for further
>>> directions will be very helpful!
>>>
>>> Let me know. Thanks!
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>>
>> --
>> *Abdullah Ishaque, BSc.*
>> MD/PhD Student, Neuroscience and Mental Health Institute
>> Faculty of Medicine and Dentistry, University of Alberta
>> aisha...@ualberta.ca
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> 

Re: [Freesurfer] mri_vol2surf warning

[Douglas N. Greve]

And what is the voxel resolution of the input to mri_vol2surf?


On 05/02/2018 03:35 PM, Rachel Bencic wrote:
>
>
> Hello,
>
> The voxel resolution of the unwarped mov volume used in bbregister was:
>
> voxel sizes: 3.75, 3.75, 5.00
>
> So the reported values in the warning appear correct.
>
> Rachel
>
>
>
> On 05/02/2018, Douglas Greve wrote:
>
> When you ran bbregister, what was the voxel resolution of the mov volume?
> On 05/02/2018 01:28 PM, Rachel Bencic wrote:
> >
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to resample beta weights generated from AFNI’s 
> > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior 
> > to running 3dDeconvolve, I ran bbregister to coregister subjects’ 
> > (unwarped) functional data to their T1 anatomical scans and to 
> > generate a registration file to be used in the mri_vol2surf command.
> >
> > However, I get the following warning when I run the mri_vol2surf command:
> >
> > WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) 
> > differs from that listed in the registration file (3.75, 3.75, 5)
> >
> > I've searched the list and came across a potentially similar case from 
> > Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which 
> > included the following advice:
> >
> > Hi Kevin, you can ignore that warning. The values in the registration
> >
> > file are not correct.
> >
> > doug
> >
> > I thought I would reach out to inquire as to whether this is still the 
> > case (i.e., that this warning can be ignored) or if it might be a more 
> > serious issue? I will add that mri_vol2surf did appear to run 
> > successfully (i.e., it did not error out) and provided a .mgh file as 
> > output.
> >
> > In case it is helpful, as a next step I plan to convert the .mgh file 
> > to an ASCII file to extract the time series. Ultimately, I plan to run 
> > graph analyses on the time series data.
> >
> > Any feedback you have would be greatly appreciated.
> >
> > Rachel
> >
> > 1) FreeSurfer version: freesurfer_6.0_x86_64
> >
> > 2) Platform: OSX High Sierra
> >
> > Here is my command:
> >
> > mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg 
> > ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh
> >
> > mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white 
> > ../lh_ascii/lh.1.asc
> >
> > And the full output:
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = lh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> >  original matrix ---
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.00.00.01.0;
> >
> >  original matrix ---
> >
> > Reading surface 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white
> >
> > Done reading source surface
> >
> > Reading thickness 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >
> > 1 0.5 0.5 0.5
> >
> > using old
> >
> > Done mapping volume to surface
> >
> > Number of source voxels hit = 8657
> >
> > Writing to ./lh.1.mgh
> >
> > Dim: 146930 1 1
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = rh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> >  original matrix ---
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.00.00.01.0;
> >
> >  original matrix ---
> >
> > Reading surface 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white
> >
> > Done reading source surface
> >
> > Reading thickness 
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >

Re: [Freesurfer] mri_vol2surf warning

[Douglas N. Greve]

When you ran bbregister, what was the voxel resolution of the mov volume?


On 05/02/2018 01:28 PM, Rachel Bencic wrote:
>
>
> Hello FreeSurfer Developers,
>
> I'm attempting to resample beta weights generated from AFNI’s 
> 3dDeconvolve command to individual subjects’ cortical surfaces. Prior 
> to running 3dDeconvolve, I ran bbregister to coregister subjects’ 
> (unwarped) functional data to their T1 anatomical scans and to 
> generate a registration file to be used in the mri_vol2surf command.
>
> However, I get the following warning when I run the mri_vol2surf command:
>
> WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75) 
> differs from that listed in the registration file (3.75, 3.75, 5)
>
> I've searched the list and came across a potentially similar case from 
> Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which 
> included the following advice:
>
> Hi Kevin, you can ignore that warning. The values in the registration
>
> file are not correct.
>
> doug
>
> I thought I would reach out to inquire as to whether this is still the 
> case (i.e., that this warning can be ignored) or if it might be a more 
> serious issue? I will add that mri_vol2surf did appear to run 
> successfully (i.e., it did not error out) and provided a .mgh file as 
> output.
>
> In case it is helpful, as a next step I plan to convert the .mgh file 
> to an ASCII file to extract the time series. Ultimately, I plan to run 
> graph analyses on the time series data.
>
> Any feedback you have would be greatly appreciated.
>
> Rachel
>
> 1) FreeSurfer version: freesurfer_6.0_x86_64
>
> 2) Platform: OSX High Sierra
>
> Here is my command:
>
> mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg 
> ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh
>
> mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white 
> ../lh_ascii/lh.1.asc
>
> And the full output:
>
> srcvol = ../betaEPI/Betas_EPIpreproc.nii
>
> srcreg = ../bbregistration.dat
>
> srcregold = 0
>
> srcwarp unspecified
>
> surf = white
>
> hemi = lh
>
> ProjFrac = 0.5
>
> thickness = thickness
>
> reshape = 0
>
> interp = nearest
>
> float2int = round
>
> GetProjMax = 0
>
> INFO: float2int code = 0
>
> Done loading volume
>
> INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> types with c_(r,a,s) = 0.
>
> Input reg is register.dat
>
> WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> differs
>
> from that listed in the registration file (3.75,3.75,5)
>
>  original matrix ---
>
> 0.99988-0.009970.01155-0.43638;
>
> -0.01472-0.430230.9026022.14351;
>
> 0.004030.902660.4303334.58801;
>
> 0.00.00.01.0;
>
>  original matrix ---
>
> Reading surface 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white
>
> Done reading source surface
>
> Reading thickness 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness
>
> Done
>
> Mapping Source Volume onto Source Subject Surface
>
> 1 0.5 0.5 0.5
>
> using old
>
> Done mapping volume to surface
>
> Number of source voxels hit = 8657
>
> Writing to ./lh.1.mgh
>
> Dim: 146930 1 1
>
> srcvol = ../betaEPI/Betas_EPIpreproc.nii
>
> srcreg = ../bbregistration.dat
>
> srcregold = 0
>
> srcwarp unspecified
>
> surf = white
>
> hemi = rh
>
> ProjFrac = 0.5
>
> thickness = thickness
>
> reshape = 0
>
> interp = nearest
>
> float2int = round
>
> GetProjMax = 0
>
> INFO: float2int code = 0
>
> Done loading volume
>
> INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR 
> types with c_(r,a,s) = 0.
>
> Input reg is register.dat
>
> WARNING: the voxel resolution in the source volume (3.75,3.75,3.75) 
> differs
>
> from that listed in the registration file (3.75,3.75,5)
>
>  original matrix ---
>
> 0.99988-0.009970.01155-0.43638;
>
> -0.01472-0.430230.9026022.14351;
>
> 0.004030.902660.4303334.58801;
>
> 0.00.00.01.0;
>
>  original matrix ---
>
> Reading surface 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white
>
> Done reading source surface
>
> Reading thickness 
> /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness
>
> Done
>
> Mapping Source Volume onto Source Subject Surface
>
> 1 0.5 0.5 0.5
>
> using old
>
> Done mapping volume to surface
>
> Number of source voxels hit = 8681
>
> Writing to ./rh.1.mgh
>
> Dim: 148618 1 1
>
>
>
> ___
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Re: [Freesurfer] mri_vol2surf

[Abdullah Ishaque]

External Email - Use Caution

 I did: mri_vol2surf --src Myelin_conformed.mgz --out C01_myelin.mgz
--regheader C01 --hemi lh --projfrac 0.5

Now I'm just getting the error "freadFloat: fread failed" a whole bunch of
times and the terminal gets stuck. Any suggestions?

I checked Myelin_conformed.mgz and loaded it with orig.mgz in freeview and
they look fine with great overlap and registration

Thanks!

On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve 
wrote:

> Specify a file format for the output (eg, C01.mgz)
>
> On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
>
> External Email - Use Caution
> Hi,
>
> Thank you for the prompt response.
>
> I used the following command:
>
> mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol
> from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5
>
> This created two files called COR-.info and COR001. I tried loaded the
> COR001 file into freeview and tksurfer, but I keep the error
> "MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory
>
> Am I making a mistake somewhere?
>
> Thanks,
>
> On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve 
> wrote:
>
>> That all looks correct. For the registration, just use --regheader C01
>>
>> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>>
>>
>> Hi,
>>
>> It's my first time using FreeSurfer and I'd like some guidance regarding
>> some of my steps.
>>
>> I'm attempting to perform myelin mapping as outlined in the paper by
>> Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from
>> each subject, sample them from the mid-cortical level to create cortical
>> myelin surface maps, and perform vertexwise and ROI based analyses.
>>
>> Here's what I've done so far:
>>
>> 1. recon-all for all the subjects
>> 2. Used bbregister to register the native T2 scans to the conformed T1
>> scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl
>> --reg register.dat --t2 (my understanding here is that this generates the
>> .dat file that has the transformation to register the T2 image to the
>> conformed orig.mgz file from subject C01)
>> 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov
>> C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers
>> the T2 to the orig.mgz file in the conformed space)
>>
>> The next step for me is to perform mri_vol2surf. My question here is,
>> which file should I select for the --srcreg flag and what should the
>> --trgsubject input be? Secondly, am I on the right track to complete the
>> analysis i.e., correct file types and my understanding of the steps?
>> Clarifications regarding these questions and any suggestions for further
>> directions will be very helpful!
>>
>> Let me know. Thanks!
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> *Abdullah Ishaque, BSc.*
> MD/PhD Student, Neuroscience and Mental Health Institute
> Faculty of Medicine and Dentistry, University of Alberta
> aisha...@ualberta.ca
>
>
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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>


-- 
*Abdullah Ishaque, BSc.*
MD/PhD Student, Neuroscience and Mental Health Institute
Faculty of Medicine and Dentistry, University of Alberta
aisha...@ualberta.ca
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Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

Specify a file format for the output (eg, C01.mgz)


On 4/24/18 3:17 PM, Abdullah Ishaque wrote:


External Email - Use Caution

Hi,

Thank you for the prompt response.

I used the following command:

mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol 
from the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5


This created two files called COR-.info and COR001. I tried loaded the 
COR001 file into freeview and tksurfer, but I keep the error 
"MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory


Am I making a mistake somewhere?

Thanks,

On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve 
> wrote:


That all looks correct. For the registration, just use --regheader C01


On 4/24/18 11:12 AM, Abdullah Ishaque wrote:



Hi,

It's my first time using FreeSurfer and I'd like some guidance
regarding some of my steps.

I'm attempting to perform myelin mapping as outlined in the paper
by Righart (2017) Ann Neurol. Overall, I want to calculate myelin
maps from each subject, sample them from the mid-cortical level
to create cortical myelin surface maps, and perform vertexwise
and ROI based analyses.

Here's what I've done so far:

1. recon-all for all the subjects
2. Used bbregister to register the native T2 scans to the
conformed T1 scans using this command: bbregister --s C01 --mov
C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding
here is that this generates the .dat file that has the
transformation to register the T2 image to the conformed orig.mgz
file from subject C01)
3. Applied the register.dat file to the native T2 using
mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg
register.dat (this registers the T2 to the orig.mgz file in the
conformed space)

The next step for me is to perform mri_vol2surf. My question here
is, which file should I select for the --srcreg flag and what
should the --trgsubject input be? Secondly, am I on the right
track to complete the analysis i.e., correct file types and my
understanding of the steps? Clarifications regarding these
questions and any suggestions for further directions will be very
helpful!

Let me know. Thanks!


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The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
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 . If the e-mail was sent
to you in error
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dispose of the e-mail.




--
*Abdullah Ishaque, BSc.*
MD/PhD Student, Neuroscience and Mental Health Institute
Faculty of Medicine and Dentistry, University of Alberta
aisha...@ualberta.ca 


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Re: [Freesurfer] mri_vol2surf

[Abdullah Ishaque]

External Email - Use Caution

Hi,

Thank you for the prompt response.

I used the following command:

mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after mri_vol2vol from
the previous step) --out C01 --regheader C01 --hemi lh --projfrac 0.5

This created two files called COR-.info and COR001. I tried loaded the
COR001 file into freeview and tksurfer, but I keep the error
"MRISalloc(8229512, 76): could allocated faces \ cannot allocate memory

Am I making a mistake somewhere?

Thanks,

On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve 
wrote:

> That all looks correct. For the registration, just use --regheader C01
>
> On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>
>
> Hi,
>
> It's my first time using FreeSurfer and I'd like some guidance regarding
> some of my steps.
>
> I'm attempting to perform myelin mapping as outlined in the paper by
> Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from
> each subject, sample them from the mid-cortical level to create cortical
> myelin surface maps, and perform vertexwise and ROI based analyses.
>
> Here's what I've done so far:
>
> 1. recon-all for all the subjects
> 2. Used bbregister to register the native T2 scans to the conformed T1
> scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl
> --reg register.dat --t2 (my understanding here is that this generates the
> .dat file that has the transformation to register the T2 image to the
> conformed orig.mgz file from subject C01)
> 3. Applied the register.dat file to the native T2 using mri_vol2vol --mov
> C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers
> the T2 to the orig.mgz file in the conformed space)
>
> The next step for me is to perform mri_vol2surf. My question here is,
> which file should I select for the --srcreg flag and what should the
> --trgsubject input be? Secondly, am I on the right track to complete the
> analysis i.e., correct file types and my understanding of the steps?
> Clarifications regarding these questions and any suggestions for further
> directions will be very helpful!
>
> Let me know. Thanks!
>
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
*Abdullah Ishaque, BSc.*
MD/PhD Student, Neuroscience and Mental Health Institute
Faculty of Medicine and Dentistry, University of Alberta
aisha...@ualberta.ca
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

That all looks correct. For the registration, just use --regheader C01


On 4/24/18 11:12 AM, Abdullah Ishaque wrote:



Hi,

It's my first time using FreeSurfer and I'd like some guidance 
regarding some of my steps.


I'm attempting to perform myelin mapping as outlined in the paper by 
Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps 
from each subject, sample them from the mid-cortical level to create 
cortical myelin surface maps, and perform vertexwise and ROI based 
analyses.


Here's what I've done so far:

1. recon-all for all the subjects
2. Used bbregister to register the native T2 scans to the conformed T1 
scans using this command: bbregister --s C01 --mov C01_T2.nii 
--init-fsl --reg register.dat --t2 (my understanding here is that this 
generates the .dat file that has the transformation to register the T2 
image to the conformed orig.mgz file from subject C01)
3. Applied the register.dat file to the native T2 using mri_vol2vol 
--mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat 
(this registers the T2 to the orig.mgz file in the conformed space)


The next step for me is to perform mri_vol2surf. My question here is, 
which file should I select for the --srcreg flag and what should the 
--trgsubject input be? Secondly, am I on the right track to complete 
the analysis i.e., correct file types and my understanding of the 
steps? Clarifications regarding these questions and any suggestions 
for further directions will be very helpful!


Let me know. Thanks!


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas N. Greve]

Hi Srishti, you will need to be much more specific to allow me to help 
you. mni152_subject is not a file that can be input to recon-all (it 
should be a dicom or nifti or mgz). If you use the same input to 
recon-all that you used to view it in spm, then the FS output should 
align with your map.


On 04/12/2018 10:41 AM, srishti goel wrote:
> mni152_subject is the file that has been used for recon-all. Our 
> collaborators had run recon-all with that file so we did not do it 
> again. As far as the 'MNI template' is concerned, I didn't do that 
> part of the analysis so I am unsure which specific file it is, but it 
> MNI 152.
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
> On Thu, Apr 12, 2018 at 10:28 AM, Douglas N. Greve 
> > wrote:
>
> What is the "MNI template" that you are using. I mean an exact file
> used. Did you use this file when you ran recon-all?
>
>
> On 04/12/2018 10:23 AM, srishti goel wrote:
> > Yeah, I am unsure where to go from here as well. So the results
> can be
> > viewed in SPM and on the MNI template space itself, since SPM
> > typically does not have a problem showing multiple images in
> different
> > sizes.
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
>   >
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve
> > 
> >>
> wrote:
> >
> >     When you use bbregister, it is expecting the input nii file to
> >     represent
> >     the actual anatomy of the subject, so it does not surprise
> me that it
> >     does not work that well. I'm not sure what to do about this
> because a
> >     meta analysis image will never have decent anatomy. In
> theory, it
> >     should
> >     be already in alignment with the mni152, but this is
> trickier than it
> >     seems. How do you usually view the results? In FSL or SPM?
> Do you view
> >     them on an anatomical image?
> >
> >
> >     On 04/12/2018 09:03 AM, srishti goel wrote:
> >     > Hi Douglas,
> >     >
> >     > The negative_allsocial_proportion.nii file has actually been
> >     converted
> >     > from a vmp file - 'negative_allsocial.vmp'. We used
> neruoelf to
> >     > convert the vmp file, option - 'export to analze' and
> 'export to
> >     > nifti'. The original vmp file represent the results of a
> >     meta-analysis.
> >     >
> >     > Let me know if that helps or you would need more information.
> >     >
> >     > Thanks!
> >     >
> >     > Best,
> >     > Srishti
> >     >
> >     > Best,
> >     > Srishti
> >     > Social/Clinical Research Specialist
> >     > Child Imaging Research and Life Experiences Lab
> >     > University of North Carolina at Chapel Hill
> >     > email (W): srish...@email.unc.edu
> 
> >      >  
> >     >>
> >     > skype: srishti.goel12
> >     >
> >     >
> >     > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve
> >     > 
> >
> >         >     wrote:
> >     >
> >     >     how was negative_allsocial_proportion.nii created?
> >     >
> >     >
> >     >     On 4/11/18 9:14 PM, srishti goel wrote:
> >     >>     Hi,
> >     >>
> >     >>     I used bbregister to register:
> >     >>     bbregister --mov negative_allsocial_proportion.nii --s
> >     >>     mni152_subject --bold --lta register.lta
> >     >>     and then viewed it using:
> >     >>     tkregisterfv --mov negative_allsocial_proportion.nii
> --reg
> >     >>     register.lta --surfs
> >     >>     It doesn't look great but it still looks okay (Screenshot
> >     attached).
> >     >>     Then I also used lta in tkregisterfv, 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas N. Greve]

What is the "MNI template" that you are using. I mean an exact file 
used. Did you use this file when you ran recon-all?


On 04/12/2018 10:23 AM, srishti goel wrote:
> Yeah, I am unsure where to go from here as well. So the results can be 
> viewed in SPM and on the MNI template space itself, since SPM 
> typically does not have a problem showing multiple images in different 
> sizes.
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
> On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve 
> > wrote:
>
> When you use bbregister, it is expecting the input nii file to
> represent
> the actual anatomy of the subject, so it does not surprise me that it
> does not work that well. I'm not sure what to do about this because a
> meta analysis image will never have decent anatomy. In theory, it
> should
> be already in alignment with the mni152, but this is trickier than it
> seems. How do you usually view the results? In FSL or SPM? Do you view
> them on an anatomical image?
>
>
> On 04/12/2018 09:03 AM, srishti goel wrote:
> > Hi Douglas,
> >
> > The negative_allsocial_proportion.nii file has actually been
> converted
> > from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to
> > convert the vmp file, option - 'export to analze' and 'export to
> > nifti'. The original vmp file represent the results of a
> meta-analysis.
> >
> > Let me know if that helps or you would need more information.
> >
> > Thanks!
> >
> > Best,
> > Srishti
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
>   >
> > skype: srishti.goel12
> >
> >
> > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve
> > 
> >>
> wrote:
> >
> >     how was negative_allsocial_proportion.nii created?
> >
> >
> >     On 4/11/18 9:14 PM, srishti goel wrote:
> >>     Hi,
> >>
> >>     I used bbregister to register:
> >>     bbregister --mov negative_allsocial_proportion.nii --s
> >>     mni152_subject --bold --lta register.lta
> >>     and then viewed it using:
> >>     tkregisterfv --mov negative_allsocial_proportion.nii --reg
> >>     register.lta --surfs
> >>     It doesn't look great but it still looks okay (Screenshot
> attached).
> >>     Then I also used lta in tkregisterfv, as:
> >>     tkregisterfv --mov negative_allsocial_proportion.nii --reg
> >>     register.lta --s mni152_subject --surfs --reg reg.deleteme.dat
> >>     In this file, the volume map still lies outside the surface.
> >>     Could you please help me resolve this issue.
> >>     I tried using register.lta file in the mri_vol2surf but the
> >>     overlay map doesn't show up again.
> >>     Thanks!
> >>
> >>     Best,
> >>     Srishti
> >>     Social/Clinical Research Specialist
> >>     Child Imaging Research and Life Experiences Lab
> >>     University of North Carolina at Chapel Hill
> >>     email (W): srish...@email.unc.edu
>   >
> >>     skype: srishti.goel12
> >>
> >>
> >>     On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve
> >>     
> >>
> wrote:
> >>
> >>         don't use --init-rr ( you don't need to spec an init in
> >>         version 6)
> >>
> >>
> >>         On 4/10/18 9:48 PM, srishti goel wrote:
> >>>         When I run bbregister, it gives me an error. Attached
> is the
> >>>         register.dat.log file for it.
> >>>         Error:
> >>>
> >>>         reading source './tmp.bbregister.91068/template.nii'...
> >>>
> >>>         mri_robust_register.bin: only pass single frame MRI source
> >>>         ./tmp.bbregister.91068/template.nii.
> >>>
> >>>
> >>>         No such file or directory
> >>>
> >>>
> >>>         Any help is greatly appreciated!
> >>>
> >>>
> >>>         Best,
> >>>         Srishti
> >>>         Social/Clinical Research Specialist
> >>>         Child Imaging Research and Life Experiences Lab
> >>>         

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[srishti goel]

Yeah, I am unsure where to go from here as well. So the results can be
viewed in SPM and on the MNI template space itself, since SPM typically
does not have a problem showing multiple images in different sizes.

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve 
wrote:

> When you use bbregister, it is expecting the input nii file to represent
> the actual anatomy of the subject, so it does not surprise me that it
> does not work that well. I'm not sure what to do about this because a
> meta analysis image will never have decent anatomy. In theory, it should
> be already in alignment with the mni152, but this is trickier than it
> seems. How do you usually view the results? In FSL or SPM? Do you view
> them on an anatomical image?
>
>
> On 04/12/2018 09:03 AM, srishti goel wrote:
> > Hi Douglas,
> >
> > The negative_allsocial_proportion.nii file has actually been converted
> > from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to
> > convert the vmp file, option - 'export to analze' and 'export to
> > nifti'. The original vmp file represent the results of a meta-analysis.
> >
> > Let me know if that helps or you would need more information.
> >
> > Thanks!
> >
> > Best,
> > Srishti
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu 
> > skype: srishti.goel12
> >
> >
> > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve
> > > wrote:
> >
> > how was negative_allsocial_proportion.nii created?
> >
> >
> > On 4/11/18 9:14 PM, srishti goel wrote:
> >> Hi,
> >>
> >> I used bbregister to register:
> >> bbregister --mov negative_allsocial_proportion.nii --s
> >> mni152_subject --bold --lta register.lta
> >> and then viewed it using:
> >> tkregisterfv --mov negative_allsocial_proportion.nii --reg
> >> register.lta --surfs
> >> It doesn't look great but it still looks okay (Screenshot attached).
> >> Then I also used lta in tkregisterfv, as:
> >> tkregisterfv --mov negative_allsocial_proportion.nii --reg
> >> register.lta --s mni152_subject --surfs --reg reg.deleteme.dat
> >> In this file, the volume map still lies outside the surface.
> >> Could you please help me resolve this issue.
> >> I tried using register.lta file in the mri_vol2surf but the
> >> overlay map doesn't show up again.
> >> Thanks!
> >>
> >> Best,
> >> Srishti
> >> Social/Clinical Research Specialist
> >> Child Imaging Research and Life Experiences Lab
> >> University of North Carolina at Chapel Hill
> >> email (W): srish...@email.unc.edu 
> >> skype: srishti.goel12
> >>
> >>
> >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve
> >> > wrote:
> >>
> >> don't use --init-rr ( you don't need to spec an init in
> >> version 6)
> >>
> >>
> >> On 4/10/18 9:48 PM, srishti goel wrote:
> >>> When I run bbregister, it gives me an error. Attached is the
> >>> register.dat.log file for it.
> >>> Error:
> >>>
> >>> reading source './tmp.bbregister.91068/template.nii'...
> >>>
> >>> mri_robust_register.bin: only pass single frame MRI source
> >>> ./tmp.bbregister.91068/template.nii.
> >>>
> >>>
> >>> No such file or directory
> >>>
> >>>
> >>> Any help is greatly appreciated!
> >>>
> >>>
> >>> Best,
> >>> Srishti
> >>> Social/Clinical Research Specialist
> >>> Child Imaging Research and Life Experiences Lab
> >>> University of North Carolina at Chapel Hill
> >>> email (W): srish...@email.unc.edu
> >>> 
> >>> skype: srishti.goel12
> >>>
> >>>
> >>> On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve
> >>> >
> wrote:
> >>>
> >>> They are not in registration. Try running bbregister to
> >>> create a registration file (lta), then pass the lta to
> >>> tkregisterfv instead of --regheader
> >>>
> >>>
> >>> On 4/9/18 11:49 PM, Bruce Fischl wrote:
>  How did you generate the registration? And give us the
>  details of what you are trying to register
>  Cheers
>  Bruce
> 
>  On Apr 8, 2018, at 2:55 PM, srishti goel
>  <23srishtig...@gmail.com
>  > wrote:
> 
> > 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas N. Greve]

When you use bbregister, it is expecting the input nii file to represent 
the actual anatomy of the subject, so it does not surprise me that it 
does not work that well. I'm not sure what to do about this because a 
meta analysis image will never have decent anatomy. In theory, it should 
be already in alignment with the mni152, but this is trickier than it 
seems. How do you usually view the results? In FSL or SPM? Do you view 
them on an anatomical image?


On 04/12/2018 09:03 AM, srishti goel wrote:
> Hi Douglas,
>
> The negative_allsocial_proportion.nii file has actually been converted 
> from a vmp file - 'negative_allsocial.vmp'. We used neruoelf to 
> convert the vmp file, option - 'export to analze' and 'export to 
> nifti'. The original vmp file represent the results of a meta-analysis.
>
> Let me know if that helps or you would need more information.
>
> Thanks!
>
> Best,
> Srishti
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
> On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve 
> > wrote:
>
> how was negative_allsocial_proportion.nii created?
>
>
> On 4/11/18 9:14 PM, srishti goel wrote:
>> Hi,
>>
>> I used bbregister to register:
>> bbregister --mov negative_allsocial_proportion.nii --s
>> mni152_subject --bold --lta register.lta
>> and then viewed it using:
>> tkregisterfv --mov negative_allsocial_proportion.nii --reg
>> register.lta --surfs
>> It doesn't look great but it still looks okay (Screenshot attached).
>> Then I also used lta in tkregisterfv, as:
>> tkregisterfv --mov negative_allsocial_proportion.nii --reg
>> register.lta --s mni152_subject --surfs --reg reg.deleteme.dat
>> In this file, the volume map still lies outside the surface.
>> Could you please help me resolve this issue.
>> I tried using register.lta file in the mri_vol2surf but the
>> overlay map doesn't show up again.
>> Thanks!
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu 
>> skype: srishti.goel12
>>
>>
>> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve
>> > wrote:
>>
>> don't use --init-rr ( you don't need to spec an init in
>> version 6)
>>
>>
>> On 4/10/18 9:48 PM, srishti goel wrote:
>>> When I run bbregister, it gives me an error. Attached is the
>>> register.dat.log file for it.
>>> Error:
>>>
>>> reading source './tmp.bbregister.91068/template.nii'...
>>>
>>> mri_robust_register.bin: only pass single frame MRI source
>>> ./tmp.bbregister.91068/template.nii.
>>>
>>>
>>> No such file or directory
>>>
>>>
>>> Any help is greatly appreciated!
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> 
>>> skype: srishti.goel12
>>>
>>>
>>> On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve
>>> > wrote:
>>>
>>> They are not in registration. Try running bbregister to
>>> create a registration file (lta), then pass the lta to
>>> tkregisterfv instead of --regheader
>>>
>>>
>>> On 4/9/18 11:49 PM, Bruce Fischl wrote:
 How did you generate the registration? And give us the
 details of what you are trying to register
 Cheers
 Bruce

 On Apr 8, 2018, at 2:55 PM, srishti goel
 <23srishtig...@gmail.com
 > wrote:

> Hi Bruce,
>
> Thanks so much for pointing that out, I totally missed
> that part.
>
> Also, the registration definitely isn't appropriate.
> Could someone please guide me how to correct this
> problem. I have attached a screenshot of how it looks
> like currently.
>
>
> 
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas Greve]

don't use --init-rr ( you don't need to spec an init in version 6)


On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the 
register.dat.log file for it.

Error:

reading source './tmp.bbregister.91068/template.nii'...

mri_robust_register.bin: only pass single frame MRI source 
./tmp.bbregister.91068/template.nii.



No such file or directory


Any help is greatly appreciated!


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve 
> wrote:


They are not in registration. Try running bbregister to create a
registration file (lta), then pass the lta to tkregisterfv instead
of --regheader


On 4/9/18 11:49 PM, Bruce Fischl wrote:

How did you generate the registration? And give us the details of
what you are trying to register
Cheers
Bruce

On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com
> wrote:


Hi Bruce,

Thanks so much for pointing that out, I totally missed that part.

Also, the registration definitely isn't appropriate.
Could someone please guide me how to correct this problem. I
have attached a screenshot of how it looks like currently.




Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl
>
wrote:

Hi Srishti

the directory you are in doesn't matter. YOu either need to
set SUBJECTS_DIR in the environment, or use --sd
 to specify the
directory that contains your subjects. I think you can also
give it the full path to a target volume if you want, but
maybe Doug can comment as he knows this stuff better than I do

cheers
Bruce



 On Sun, 8 Apr 2018, srishti goel wrote:

When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which
I am submitting this command has the
mni152_subject directory within which there are all the
other required directories such as: mri,
stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu

skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve
>
wrote:
      Those commands look ok. My suspicion goes to the
use of --regheader. See
      whether the registration is ok with

      tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
      mni152_subject --surfs --reg reg.deleteme.dat


      On 04/05/2018 08:34 AM, srishti goel wrote:
      > Hi,
      >
      > I am trying to compare my volume maps
      > (negative_allsocial_proportion.nii) to someone
else's
      > (SN_like_cortical_lh.nii.gz) who have it on a
surface
      > (mni152_subject). So I used the steps for
mri_vol2surf command as
      > follows:
      >
      > Commands:
      > mri_vol2surf --src
negative_allsocial_proportion.nii --regheader
      > mni152_subject --hemi lh --o
./neg_allsocial_lh.nii --projfrac 0.5
      > Then to view it:
      > tksurfer mni152_subject lh inflated -overlay
./neg_allsocial_lh.nii
      > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
      >
      > Everything ran fine and we didn't get any error
but then while viewing
      > the files we could not see our map
(neg_allsocail_lh.nii) on the
      > surface. This file seemed to work fine as it is
not an empty file when
      > I checked the 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[srishti goel]

When I run bbregister, it gives me an error. Attached is the
register.dat.log file for it.
Error:

reading source './tmp.bbregister.91068/template.nii'...

mri_robust_register.bin: only pass single frame MRI source
./tmp.bbregister.91068/template.nii.


No such file or directory


Any help is greatly appreciated!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve 
wrote:

> They are not in registration. Try running bbregister to create a
> registration file (lta), then pass the lta to tkregisterfv instead of
> --regheader
>
> On 4/9/18 11:49 PM, Bruce Fischl wrote:
>
> How did you generate the registration? And give us the details of what you
> are trying to register
> Cheers
> Bruce
>
> On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote:
>
> Hi Bruce,
>
> Thanks so much for pointing that out, I totally missed that part.
>
> Also, the registration definitely isn't appropriate.
> Could someone please guide me how to correct this problem. I have attached
> a screenshot of how it looks like currently.
>
>
> 
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl 
> wrote:
>
>> Hi Srishti
>>
>> the directory you are in doesn't matter. YOu either need to set
>> SUBJECTS_DIR in the environment, or use --sd  to specify the
>> directory that contains your subjects. I think you can also give it the
>> full path to a target volume if you want, but maybe Doug can comment as he
>> knows this stuff better than I do
>>
>> cheers
>> Bruce
>>
>>
>>
>>  On Sun, 8 Apr 2018, srishti goel wrote:
>>
>> When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii
>>> --regheader --s
>>> mni152_subject --surfs --reg reg.deleteme.dat
>>>
>>> It gives me the error: cannot find mni152_subject.
>>> Although I clearly checked that the directory from which I am submitting
>>> this command has the
>>> mni152_subject directory within which there are all the other required
>>> directories such as: mri,
>>> stats, surf, scripts, etc.
>>>
>>> I am unsure what is happening here.
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <
>>> dgr...@mgh.harvard.edu> wrote:
>>>   Those commands look ok. My suspicion goes to the use of
>>> --regheader. See
>>>   whether the registration is ok with
>>>
>>>   tkregisterfv --mov negative_allsocial_proportion.nii --regheader
>>> --s
>>>   mni152_subject --surfs --reg reg.deleteme.dat
>>>
>>>
>>>   On 04/05/2018 08:34 AM, srishti goel wrote:
>>>   > Hi,
>>>   >
>>>   > I am trying to compare my volume maps
>>>   > (negative_allsocial_proportion.nii) to someone else's
>>>   > (SN_like_cortical_lh.nii.gz) who have it on a surface
>>>   > (mni152_subject). So I used the steps for mri_vol2surf command as
>>>   > follows:
>>>   >
>>>   > Commands:
>>>   > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
>>>   > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac
>>> 0.5
>>>   > Then to view it:
>>>   > tksurfer mni152_subject lh inflated -overlay
>>> ./neg_allsocial_lh.nii
>>>   > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
>>>   >
>>>   > Everything ran fine and we didn't get any error but then while
>>> viewing
>>>   > the files we could not see our map (neg_allsocail_lh.nii) on the
>>>   > surface. This file seemed to work fine as it is not an empty
>>> file when
>>>   > I checked the file size. However, when we view it using tksurfer
>>> it
>>>   > does not show up as a highlighted portion on the surface. The
>>>   > SN_like_cortical_lh.nii.gz file shows up just fine.
>>>   >
>>>   > Could someone please help me figure out what might have gone
>>> wrong here.
>>>   >
>>>   > Thanks so much!
>>>   >
>>>   >
>>>   >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas Greve]

They are not in registration. Try running bbregister to create a 
registration file (lta), then pass the lta to tkregisterfv instead of 
--regheader



On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what 
you are trying to register

Cheers
Bruce

On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com 
> wrote:



Hi Bruce,

Thanks so much for pointing that out, I totally missed that part.

Also, the registration definitely isn't appropriate.
Could someone please guide me how to correct this problem. I have 
attached a screenshot of how it looks like currently.





Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl 
> wrote:


Hi Srishti

the directory you are in doesn't matter. YOu either need to set
SUBJECTS_DIR in the environment, or use --sd  to
specify the
directory that contains your subjects. I think you can also give
it the full path to a target volume if you want, but maybe Doug
can comment as he knows this stuff better than I do

cheers
Bruce



 On Sun, 8 Apr 2018, srishti goel wrote:

When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which I
am submitting this command has the
mni152_subject directory within which there are all the other
required directories such as: mri,
stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve
> wrote:
      Those commands look ok. My suspicion goes to the use of
--regheader. See
      whether the registration is ok with

      tkregisterfv --mov negative_allsocial_proportion.nii
--regheader --s
      mni152_subject --surfs --reg reg.deleteme.dat


      On 04/05/2018 08:34 AM, srishti goel wrote:
      > Hi,
      >
      > I am trying to compare my volume maps
      > (negative_allsocial_proportion.nii) to someone else's
      > (SN_like_cortical_lh.nii.gz) who have it on a surface
      > (mni152_subject). So I used the steps for
mri_vol2surf command as
      > follows:
      >
      > Commands:
      > mri_vol2surf --src negative_allsocial_proportion.nii
--regheader
      > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii
--projfrac 0.5
      > Then to view it:
      > tksurfer mni152_subject lh inflated -overlay
./neg_allsocial_lh.nii
      > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
      >
      > Everything ran fine and we didn't get any error but
then while viewing
      > the files we could not see our map
(neg_allsocail_lh.nii) on the
      > surface. This file seemed to work fine as it is not
an empty file when
      > I checked the file size. However, when we view it
using tksurfer it
      > does not show up as a highlighted portion on the
surface. The
      > SN_like_cortical_lh.nii.gz file shows up just fine.
      >
      > Could someone please help me figure out what might
have gone wrong here.
      >
      > Thanks so much!
      >
      >
      >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Bruce Fischl]

How did you generate the registration? And give us the details of what you are 
trying to register
Cheers 
Bruce

> On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote:
> 
> Hi Bruce,
> 
> Thanks so much for pointing that out, I totally missed that part.
> 
> Also, the registration definitely isn't appropriate.
> Could someone please guide me how to correct this problem. I have attached a 
> screenshot of how it looks like currently.
> 
> 
> 
> 
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
> 
> 
>> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl  
>> wrote:
>> Hi Srishti
>> 
>> the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR 
>> in the environment, or use --sd  to specify the
>> directory that contains your subjects. I think you can also give it the full 
>> path to a target volume if you want, but maybe Doug can comment as he knows 
>> this stuff better than I do
>> 
>> cheers
>> Bruce
>> 
>> 
>> 
>>  On Sun, 8 Apr 2018, srishti goel wrote:
>> 
>>> When I type this command:tkregisterfv --mov 
>>> negative_allsocial_proportion.nii --regheader --s
>>> mni152_subject --surfs --reg reg.deleteme.dat
>>> 
>>> It gives me the error: cannot find mni152_subject.
>>> Although I clearly checked that the directory from which I am submitting 
>>> this command has the
>>> mni152_subject directory within which there are all the other required 
>>> directories such as: mri,
>>> stats, surf, scripts, etc.
>>> 
>>> I am unsure what is happening here.
>>> 
>>> 
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>> 
>>> 
>>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve  
>>> wrote:
>>>   Those commands look ok. My suspicion goes to the use of --regheader. 
>>> See
>>>   whether the registration is ok with
>>> 
>>>   tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
>>>   mni152_subject --surfs --reg reg.deleteme.dat
>>> 
>>> 
>>>   On 04/05/2018 08:34 AM, srishti goel wrote:
>>>   > Hi,
>>>   >
>>>   > I am trying to compare my volume maps
>>>   > (negative_allsocial_proportion.nii) to someone else's
>>>   > (SN_like_cortical_lh.nii.gz) who have it on a surface
>>>   > (mni152_subject). So I used the steps for mri_vol2surf command as
>>>   > follows:
>>>   >
>>>   > Commands:
>>>   > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
>>>   > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
>>>   > Then to view it:
>>>   > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii
>>>   > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
>>>   >
>>>   > Everything ran fine and we didn't get any error but then while 
>>> viewing
>>>   > the files we could not see our map (neg_allsocail_lh.nii) on the
>>>   > surface. This file seemed to work fine as it is not an empty file 
>>> when
>>>   > I checked the file size. However, when we view it using tksurfer it
>>>   > does not show up as a highlighted portion on the surface. The
>>>   > SN_like_cortical_lh.nii.gz file shows up just fine.
>>>   >
>>>   > Could someone please help me figure out what might have gone wrong 
>>> here.
>>>   >
>>>   > Thanks so much!
>>>   >
>>>   >
>>>   >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>> 
>>> 
>>> 
>> 
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>> 
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>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Bruce Fischl]

Hi Srishti

the directory you are in doesn't matter. YOu either need to set 
SUBJECTS_DIR in the environment, or use --sd  to specify the
directory that contains your subjects. I think you can also give it the 
full path to a target volume if you want, but maybe Doug can comment as he 
knows this stuff better than I do


cheers
Bruce


 On Sun, 8 Apr 2018, srishti goel 
wrote:



When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii 
--regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which I am submitting this 
command has the
mni152_subject directory within which there are all the other required 
directories such as: mri,
stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve  
wrote:
  Those commands look ok. My suspicion goes to the use of --regheader. See
  whether the registration is ok with

  tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
  mni152_subject --surfs --reg reg.deleteme.dat


  On 04/05/2018 08:34 AM, srishti goel wrote:
  > Hi,
  >
  > I am trying to compare my volume maps
  > (negative_allsocial_proportion.nii) to someone else's
  > (SN_like_cortical_lh.nii.gz) who have it on a surface
  > (mni152_subject). So I used the steps for mri_vol2surf command as
  > follows:
  >
  > Commands:
  > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
  > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
  > Then to view it:
  > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii
  > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
  >
  > Everything ran fine and we didn't get any error but then while viewing
  > the files we could not see our map (neg_allsocail_lh.nii) on the
  > surface. This file seemed to work fine as it is not an empty file when
  > I checked the file size. However, when we view it using tksurfer it
  > does not show up as a highlighted portion on the surface. The
  > SN_like_cortical_lh.nii.gz file shows up just fine.
  >
  > Could someone please help me figure out what might have gone wrong here.
  >
  > Thanks so much!
  >
  >
  >
> ___
> Freesurfer mailing list
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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[srishti goel]

When I type this command:
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which I am submitting
this command has the mni152_subject directory within which there are all
the other required directories such as: mri, stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve 
wrote:

> Those commands look ok. My suspicion goes to the use of --regheader. See
> whether the registration is ok with
>
> tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
> mni152_subject --surfs --reg reg.deleteme.dat
>
>
> On 04/05/2018 08:34 AM, srishti goel wrote:
> > Hi,
> >
> > I am trying to compare my volume maps
> > (negative_allsocial_proportion.nii) to someone else's
> > (SN_like_cortical_lh.nii.gz) who have it on a surface
> > (mni152_subject). So I used the steps for mri_vol2surf command as
> > follows:
> >
> > Commands:
> > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
> > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
> > Then to view it:
> > tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii
> > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
> >
> > Everything ran fine and we didn't get any error but then while viewing
> > the files we could not see our map (neg_allsocail_lh.nii) on the
> > surface. This file seemed to work fine as it is not an empty file when
> > I checked the file size. However, when we view it using tksurfer it
> > does not show up as a highlighted portion on the surface. The
> > SN_like_cortical_lh.nii.gz file shows up just fine.
> >
> > Could someone please help me figure out what might have gone wrong here.
> >
> > Thanks so much!
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas N. Greve]

Those commands look ok. My suspicion goes to the use of --regheader. See 
whether the registration is ok with

tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s 
mni152_subject --surfs --reg reg.deleteme.dat


On 04/05/2018 08:34 AM, srishti goel wrote:
> Hi,
>
> I am trying to compare my volume maps 
> (negative_allsocial_proportion.nii) to someone else's 
> (SN_like_cortical_lh.nii.gz) who have it on a surface 
> (mni152_subject). So I used the steps for mri_vol2surf command as 
> follows:
>
> Commands:
> mri_vol2surf --src negative_allsocial_proportion.nii --regheader 
> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5
> Then to view it:
> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii 
> -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
>
> Everything ran fine and we didn't get any error but then while viewing 
> the files we could not see our map (neg_allsocail_lh.nii) on the 
> surface. This file seemed to work fine as it is not an empty file when 
> I checked the file size. However, when we view it using tksurfer it 
> does not show up as a highlighted portion on the surface. The 
> SN_like_cortical_lh.nii.gz file shows up just fine.
>
> Could someone please help me figure out what might have gone wrong here.
>
> Thanks so much!
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

[Charlotte Grosse Wiesmann]

Hi Doug,

great, this works well, thank you very much!

Best

Charlotte

- Original Message -
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, March 14, 2018 11:37:13 PM
Subject: Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

You should be able to use --regheader ANTSaverage (assuming ANTSaverage 
is the name you gave it when running recon-all)

On 03/12/2018 01:32 PM, Charlotte Grosse Wiesmann wrote:
> Hi Doug,
>
> I was trying to map my volume mask from my study-specific average subject 
> template space to the surface (still in my average subject template space) 
> with mri_vol2surf as you suggested below. How d I get the correct 
> register.dat file do do this?
>
> I have tried bbregister but am not sure what subject and what moveable volume 
> I need to take since I am basically staying in the same space (my own average 
> subject space).
>
> I am stuck with my analysis on this and would highly appreciate your help!
>
> Thank you very much in advance!
>
> Charlotte
>
>
> - Original Message -
> From: "wiesmann" <wiesm...@cbs.mpg.de>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Friday, February 9, 2018 7:45:35 PM
> Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume 
> mask to the surface space for mri_mcsim using my own template?
>
> Hi Doug,
>
> thank you very much for your help! I am sorry for the naive questions, but I 
> am not very familiar with surface analyses:
> I ran recon-all on my template ("ANTSaverage") so that I have the surfaces.
> Is it correct that I have registered my volume mask to my template space 
> before I map it onto the surface with mri_vol2surf?
> And where do I get the registration file from to run mri_vol2surf?
>
> I am also not quite sure I understand why I have to register the surface mask 
> to fsaverage then rather than to my own template?
>
> I am sorry for these questions, but I am a bit confused and would really 
> appreciate your help!
>
> Charlotte
>
>
> - Original Message -
> From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Saturday, February 3, 2018 8:58:49 PM
> Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume 
> mask to the surface space for mri_mcsim using my own template?
>
> You need to map the mask into the fsaverage space. Probably the easiest
> way to do this is to run recon-all on your template to get surfaces.
> Then run mri_vol2surf to map your mask onto the surface, then use
> mris_apply_reg to map your surface mask to fsaverage (make sure to
> --no-rev since you are mapping a mask). If you want to do FDR, then run
> mri_fdr.
>
>
> On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:
>> Dear freesurfer experts,
>>
>> I would like to restrict my surface analyses (cortical thickness and surface 
>> area) to a mask from an fMRI meta-analysis using my own subject-specific 
>> template that I created with ANTS. So far, I have used Qdec and wanted to 
>> correct for cluster size running the Monte Carlo (MC) simulation on my own 
>> template.
>> Now I would like to restrict the simulation to my mask to do a small volume 
>> correction in my regions of interest. I mapped the mask to my own template 
>> (in volume space) using ANTS (WarpImageMultiTransform) but how can I get 
>> this mask to the surface space to run the MC simulation on my own template 
>> within this mask?
>>
>> I was planning to do:
>> mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z 
>> --surface my_template ?h --nreps 1 --mask mymask.mgz
>>
>> How do I get mymask.mgz in the correct space for this?
>>
>> And can I continue using Qdec or do I have to use glmfit for these analyses?
>>
>> In addition: is it also possible to do a small volume correction using FDR 
>> rather than cluster-size correction?
>>
>> Thanks for your help!
>>
>> Charlotte
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you i

Re: [Freesurfer] mri_vol2surf - what register.dat file to use?

[Douglas N. Greve]

You should be able to use --regheader ANTSaverage (assuming ANTSaverage 
is the name you gave it when running recon-all)

On 03/12/2018 01:32 PM, Charlotte Grosse Wiesmann wrote:
> Hi Doug,
>
> I was trying to map my volume mask from my study-specific average subject 
> template space to the surface (still in my average subject template space) 
> with mri_vol2surf as you suggested below. How d I get the correct 
> register.dat file do do this?
>
> I have tried bbregister but am not sure what subject and what moveable volume 
> I need to take since I am basically staying in the same space (my own average 
> subject space).
>
> I am stuck with my analysis on this and would highly appreciate your help!
>
> Thank you very much in advance!
>
> Charlotte
>
>
> - Original Message -
> From: "wiesmann" 
> To: "Freesurfer support list" 
> Sent: Friday, February 9, 2018 7:45:35 PM
> Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume 
> mask to the surface space for mri_mcsim using my own template?
>
> Hi Doug,
>
> thank you very much for your help! I am sorry for the naive questions, but I 
> am not very familiar with surface analyses:
> I ran recon-all on my template ("ANTSaverage") so that I have the surfaces.
> Is it correct that I have registered my volume mask to my template space 
> before I map it onto the surface with mri_vol2surf?
> And where do I get the registration file from to run mri_vol2surf?
>
> I am also not quite sure I understand why I have to register the surface mask 
> to fsaverage then rather than to my own template?
>
> I am sorry for these questions, but I am a bit confused and would really 
> appreciate your help!
>
> Charlotte
>
>
> - Original Message -
> From: "Douglas Greve" 
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Saturday, February 3, 2018 8:58:49 PM
> Subject: Re: [Freesurfer] REPOST: mri_mcsim with mask - How do I map a volume 
> mask to the surface space for mri_mcsim using my own template?
>
> You need to map the mask into the fsaverage space. Probably the easiest
> way to do this is to run recon-all on your template to get surfaces.
> Then run mri_vol2surf to map your mask onto the surface, then use
> mris_apply_reg to map your surface mask to fsaverage (make sure to
> --no-rev since you are mapping a mask). If you want to do FDR, then run
> mri_fdr.
>
>
> On 1/29/18 12:17 PM, Charlotte Grosse Wiesmann wrote:
>> Dear freesurfer experts,
>>
>> I would like to restrict my surface analyses (cortical thickness and surface 
>> area) to a mask from an fMRI meta-analysis using my own subject-specific 
>> template that I created with ANTS. So far, I have used Qdec and wanted to 
>> correct for cluster size running the Monte Carlo (MC) simulation on my own 
>> template.
>> Now I would like to restrict the simulation to my mask to do a small volume 
>> correction in my regions of interest. I mapped the mask to my own template 
>> (in volume space) using ANTS (WarpImageMultiTransform) but how can I get 
>> this mask to the surface space to run the MC simulation on my own template 
>> within this mask?
>>
>> I was planning to do:
>> mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z 
>> --surface my_template ?h --nreps 1 --mask mymask.mgz
>>
>> How do I get mymask.mgz in the correct space for this?
>>
>> And can I continue using Qdec or do I have to use glmfit for these analyses?
>>
>> In addition: is it also possible to do a small volume correction using FDR 
>> rather than cluster-size correction?
>>
>> Thanks for your help!
>>
>> Charlotte
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> 

Re: [Freesurfer] mri_vol2surf wrong hemisphere

[Defenderfer, Matthew K]

Hi Doug,


FSLView gives a label of L and R and the parcels on the LH in fslview match the 
LH parcels in their included Excel spreadsheet. That's really all the 
verification I have for it right now. It's possible they switched the 
hemispheres when they made the original parcellation volume before making the 
excel sheet, but I don't know how likely that is. Is there anything I can do to 
help out with this?


-Matt


Matthew K. Defenderfer B.S. | Graduate Research Assistant

Graduate Biomedical Sciences | Neuroscience

UAB | The University of Alabama at Birmingham

Laboratory of Kristina Visscher, PhD

Department of Neurobiology

CIRC 111 | C: (865) 805-6389



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve 
<gr...@nmr.mgh.harvard.edu>
Sent: Monday, December 4, 2017 11:46:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere

How do you know what is right and left in the volume?


On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to
> use the parcellation from Gordon et al. 2014
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs
> for the frontoparietal network. They provided a volume of the
> parcellation in MNI152 space for public use. I took this volume and
> applied the mri_vol2surf command to it to create 2 overlays of the
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the
> RH on the surface and vice versa. This is a problem since the
> parcellation is not symmetric across hemispheres.This is not a problem
> with the volume either as I looked at it overlayed with the MNI152
> brain in fslview and saw that the parcels were on the correct
> hemisphere. Another problem is that 1 of the frontoparietal parcels,
> number 24, was not found on the surface of either hemisphere after
> turning it to a surface. I don't know why this would be the case since
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the
> left hemisphere. After running essentially the same vol2surf command
> as above, the ROI only appeared on the RH surface. I am using
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. | Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_vol2surf wrong hemisphere

[Douglas N Greve]

How do you know what is right and left in the volume?


On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to 
> use the parcellation from Gordon et al. 2014 
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs 
> for the frontoparietal network. They provided a volume of the 
> parcellation in MNI152 space for public use. I took this volume and 
> applied the mri_vol2surf command to it to create 2 overlays of the 
> parcels, 1 for each hemisphere. The code was:
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage 
> --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh
>
> mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage 
> --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh
>
> The code ran, but the LH parcels in the volume were transferred to the 
> RH on the surface and vice versa. This is a problem since the 
> parcellation is not symmetric across hemispheres.This is not a problem 
> with the volume either as I looked at it overlayed with the MNI152 
> brain in fslview and saw that the parcels were on the correct 
> hemisphere. Another problem is that 1 of the frontoparietal parcels, 
> number 24, was not found on the surface of either hemisphere after 
> turning it to a surface. I don't know why this would be the case since 
> there are all cortical parcels.
>
> I have also tried this with a volume ROI that is only located on the 
> left hemisphere. After running essentially the same vol2surf command 
> as above, the ROI only appeared on the RH surface. I am using 
> mri_vol2surf from Freesurfer v6.0.0
>
>
> Any help would be greatly appreciated. Thank you!
>
> Best,
> Matthew Defenderfer
>
>
> *Matthew K. Defenderfer B.S. | Graduate Research Assistant*
>
> Graduate Biomedical Sciences|Neuroscience
>
> UAB | The University of Alabama at Birmingham
>
> Laboratory of Kristina Visscher, PhD
>
> Department of Neurobiology
>
> CIRC 111 | C: (865) 805-6389
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

probably youu'll want to sample it in the middle of the cortical ribbon, 
so --projfrac 0.5



On 8/22/17 12:11 PM, John Anderson wrote:



Thank you for the response

It is FDG SUV map


need more info, eg, what kind of map is that? what modality?


 Original Message 
Subject: mri_vol2surf
Local Time: August 22, 2017 11:04 AM
UTC Time: August 22, 2017 3:04 PM
From: john.ande...@protonmail.com
To: Freesurfer support list 

Dear FS experts,
I ran voxel-wise analysis between two groups using randomise in FSL 
and the final statistical maps is as attached.
 I aim to to repeat the analysis using surface based analysis. I 
followed the steps as in wiki. I am not sure what is the correct 
value for projfrac int he command "mri_vol2surf"  that is more 
appropriate to show the findings that I have in the voxel-wise (more 
int eh white matter) on surface.


Thank you for any suggestion
John







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Re: [Freesurfer] mri_vol2surf

[John Anderson]

> Thank you for the response
>
> It is FDG SUV map
>
> need more info, eg, what kind of map is that? what modality?
>
>>  Original Message 
>> Subject: mri_vol2surf
>> Local Time: August 22, 2017 11:04 AM
>> UTC Time: August 22, 2017 3:04 PM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list 
>>
>> Dear FS experts,
>> I ran voxel-wise analysis between two groups using randomise in FSL and the 
>> final statistical maps is as attached.
>>  I aim to to repeat the analysis using surface based analysis. I followed 
>> the steps as in wiki. I am not sure what is the correct value for projfrac 
>> int he command "mri_vol2surf"  that is more appropriate to show the findings 
>> that I have in the voxel-wise (more int eh white matter) on surface.
>>
>> Thank you for any suggestion
>> John___
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Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

need more info, eg, what kind of map is that? what modality?


On 8/22/17 11:04 AM, John Anderson wrote:

Dear FS experts,
I ran voxel-wise analysis between two groups using randomise in FSL 
and the final statistical maps is as attached.
 I aim to to repeat the analysis using surface based analysis. I 
followed the steps as in wiki. I am not sure what is the correct value 
for projfrac int he command "mri_vol2surf"  that is more appropriate 
to show the findings that I have in the voxel-wise (more int eh white 
matter) on surface.


Thank you for any suggestion
John



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Re: [Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

[Elijah Mak]

Hi Freesurfer Team,

No worries, I have found a helpful solution from an old thread using
mris_expand.


http://i.imgur.com/CrF125X.png

Thanks.

Best Wishes,
Elijah

On Tue, Jun 13, 2017 at 8:47 PM, Elijah Mak  wrote:

> Hi Freesurfer Team,
>
> Is there a way to visualise the sampling edges across a range of projfrac
> values (0.1 (closer to WM) - 0.5) and overlay them onto PET data?
>
> Any suggestions are greatly appreciated. Thanks.
>
> Best Wishes,
> Elijah
>
>
>


-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] mri_vol2surf error in FS6

[VA Research]

; > > Trace/BPT trap
> > > > ERROR: input file must be in NIfTI format
> > > > Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon
> > Jan  9
> > > > 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64
> > x86_64
> > > >
> > > >
> > > > i ran sudo -E fs_update as described on
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>
> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>>
> > > >
> > > > but still get the same error
> > > >
> > > > Were you guys able to resolve this issue?
> > > >
> > > > Thanks so much
> > > >
> > > > joseph
> > > >
> > > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado
> > <ladof...@gmail.com <mailto:ladof...@gmail.com>
> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>
> > > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>
> > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>>> wrote:
> > > >
> > > > yes, I have the /Applications/freesurfer/lib/gcc
> > > > directory.(actually, ‘had’ as I reinstalled 5.3)   I
> installed 6.0
> > > > on top of 5.3 without uninstalling 5.3 first, so it was
> not a clean
> > > > install.  I will try a clean re-install with the tar
> file with the
> > > > steps you suggest. Thanks.
> > > >
> > > > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> > > > From: zkauf...@nmr.mgh.harvard.edu  zkauf...@nmr.mgh.harvard.edu>
> > > <mailto:zkauf...@nmr.mgh.harvard.edu <mailto:zkauf...@nmr.mgh.
> harvard.edu>>
> > > <mailto:zkauf...@nmr.mgh.harvard.edu
> > <mailto:zkauf...@nmr.mgh.harvard.edu>
> > > <mailto:zkauf...@nmr.mgh.harvard.edu <mailto:zkauf...@nmr.mgh.
> harvard.edu>>>
> > > > Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> > > > To: "Freesurfer support list" <
> freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > > Cc: freesurfer@nmr.mgh.harvard.edu  freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu  freesurfer@nmr.mgh.harvard.edu>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu  freesurfer@nmr.mgh.harvard.edu>>>
> > > > Message-ID:
> > > >
> > > >
> > >  <62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu>
> > > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu>>
> > > >
> > >
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu>
> > >
> >  <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu>>>>
> > > > Content-Type: text/plain;charset=iso-8859-1
> > > >
> > > > Hello Fred,
> > > >
> > > > Do you have the /Applications/freesurfer/lib/gcc
> directory?
> > > 

Re: [Freesurfer] mri_vol2surf error in FS6

[Z K]

 > but still get the same error
> > >
> > > Were you guys able to resolve this issue?
> > >
> > > Thanks so much
> > >
> > > joseph
> > >
> > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado
> <ladof...@gmail.com <mailto:ladof...@gmail.com>
> > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>
> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>
> <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>>> wrote:
> >     >
> > > yes, I have the /Applications/freesurfer/lib/gcc
> > > directory.(actually, ‘had’ as I reinstalled 5.3)   I 
> installed 6.0
> > > on top of 5.3 without uninstalling 5.3 first, so it was not a 
> clean
> > > install.  I will try a clean re-install with the tar file 
> with the
> > > steps you suggest. Thanks.
> > >
> > > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> > > From: zkauf...@nmr.mgh.harvard.edu 
> <mailto:zkauf...@nmr.mgh.harvard.edu>
> > <mailto:zkauf...@nmr.mgh.harvard.edu 
> <mailto:zkauf...@nmr.mgh.harvard.edu>>
> > <mailto:zkauf...@nmr.mgh.harvard.edu
> <mailto:zkauf...@nmr.mgh.harvard.edu>
> > <mailto:zkauf...@nmr.mgh.harvard.edu 
> <mailto:zkauf...@nmr.mgh.harvard.edu>>>
> > > Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > Cc: freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > Message-ID:
> > >
> > >
> >  <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
> > 
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>>
> > >
> >
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
> >
>  <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> 
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>>>>
> > > Content-Type: text/plain;charset=iso-8859-1
> > >
> > > Hello Fred,
> > >
> > > Do you have the /Applications/freesurfer/lib/gcc directory?
> > Also, out of
> > > curiosity, did freesurfer 5.3 exist on your system before
> > installed 6.0?
> > > That error shouldnt happen if FS6 is cleanly installed and
> > definitely
> > > shouldnt happen of SIPS is disabled.
> > >
> > > I suppose as a last resort could you just completely
> remove FS
> > from your
> > > machine and just install it directly from the tar file
> (save the
> > > license.txt file):
> > >
> > >
> >
>  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
> 
> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz>
> >
>  
> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
> 
> <ftp://surfer.nmr.mgh.harvard.ed

Re: [Freesurfer] mri_vol2surf error in FS6

[VA Research]

disabled SIP got it working

briefly why would SIP (files system not accessible) halt the trac-all?



On Tue, Mar 28, 2017 at 12:59 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote:

> Thanks for the log file. I believe this is a real bug on OSX platforms.
> I should have a fix by tomorrow.
>
> -Zeke
>
> On 03/28/2017 03:46 PM, VA Research wrote:
> > I will try to disable SIP
> >
> > (although i dont want to restart the system because i am curious if this
> > XL defect will ever be corrected running 80 plus hours now... lol)
> >
> > attached is the trac -all.log
> >
> > On Tue, Mar 28, 2017 at 12:40 PM, Z K <zkauf...@nmr.mgh.harvard.edu
> > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:
> >
> > This error is related a new security feature implemented in OS X El
> > Capitan:
> >
> >https://support.apple.com/en-gb/HT204899
> > <https://support.apple.com/en-gb/HT204899>
> >
> > You should not be getting this error with version FS6.0, but if you
> are
> > you can always get around it by disabling SIP:
> >
> >
> > http://osxdaily.com/2015/10/05/disable-rootless-system-
> integrity-protection-mac-os-x/
> > <http://osxdaily.com/2015/10/05/disable-rootless-system-
> integrity-protection-mac-os-x/>
> >
> > However, I am still curious how/why you are getting this error. Is
> there
> > a trac-all .log file somewhere you can send me so I can see at what
> > point exactly this error occurs?
> >
> > -Zeke
> >
> >
> >
> > On 03/28/2017 03:29 PM, VA Research wrote:
> > > Hello,
> > >
> > > i am on el capitan 10.11.6 ,  XQuartz 2.7.8
> > >
> > > I named the old Applictions/freesurfer directory something else and
> > > installed freesurfer 6.0 and sourced through the script, i also
> > changed
> > > the subject directory
> > >
> > > but otherwise i think this is a clean install of FS 6.0
> > >
> > >
> > >  I am running trac-all -prep
> > >
> > > and am getting the same error
> > >
> > > dyld: lazy symbol binding failed: Symbol not found:
> > ___emutls_get_address
> > >   Referenced from:
> > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> > >   Expected in: /usr/lib/libSystem.B.dylib
> > >
> > > dyld: Symbol not found: ___emutls_get_address
> > >   Referenced from:
> > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> > >   Expected in: /usr/lib/libSystem.B.dylib
> > >
> > > Trace/BPT trap
> > > ERROR: input file must be in NIfTI format
> > > Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan  9
> > > 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64
> > >
> > >
> > > i ran sudo -E fs_update as described on
> > > https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>
> > >
> > > but still get the same error
> > >
> > > Were you guys able to resolve this issue?
> > >
> > > Thanks so much
> > >
> > > joseph
> > >
> > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladof...@gmail.com
> > <mailto:ladof...@gmail.com>
> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>> wrote:
> > >
> > > yes, I have the /Applications/freesurfer/lib/gcc
> > > directory.(actually, ‘had’ as I reinstalled 5.3)   I installed
> 6.0
> > > on top of 5.3 without uninstalling 5.3 first, so it was not a
> clean
> > > install.  I will try a clean re-install with the tar file with
> the
> > > steps you suggest. Thanks.
> > >
> > > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> > > From: zkauf...@nmr.mgh.harvard.edu
> > <mailto:zkauf...@nmr.mgh.harvard.edu>
> > <mailto:zkauf...@nmr.mgh.harvard.edu
> > <mailto:zkauf...@nmr.mgh.harvard.edu>>
> > > Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.

Re: [Freesurfer] mri_vol2surf error in FS6

[Z K]

Thanks for the log file. I believe this is a real bug on OSX platforms. 
I should have a fix by tomorrow.

-Zeke

On 03/28/2017 03:46 PM, VA Research wrote:
> I will try to disable SIP
>
> (although i dont want to restart the system because i am curious if this
> XL defect will ever be corrected running 80 plus hours now... lol)
>
> attached is the trac -all.log
>
> On Tue, Mar 28, 2017 at 12:40 PM, Z K <zkauf...@nmr.mgh.harvard.edu
> <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:
>
> This error is related a new security feature implemented in OS X El
> Capitan:
>
>https://support.apple.com/en-gb/HT204899
> <https://support.apple.com/en-gb/HT204899>
>
> You should not be getting this error with version FS6.0, but if you are
> you can always get around it by disabling SIP:
>
>
> 
> http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
> 
> <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/>
>
> However, I am still curious how/why you are getting this error. Is there
> a trac-all .log file somewhere you can send me so I can see at what
> point exactly this error occurs?
>
> -Zeke
>
>
>
> On 03/28/2017 03:29 PM, VA Research wrote:
> > Hello,
> >
> > i am on el capitan 10.11.6 ,  XQuartz 2.7.8
> >
> > I named the old Applictions/freesurfer directory something else and
> > installed freesurfer 6.0 and sourced through the script, i also
> changed
> > the subject directory
> >
> > but otherwise i think this is a clean install of FS 6.0
> >
> >
> >  I am running trac-all -prep
> >
> > and am getting the same error
> >
> > dyld: lazy symbol binding failed: Symbol not found:
> ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> >
> > dyld: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> >
> > Trace/BPT trap
> > ERROR: input file must be in NIfTI format
> > Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan  9
> > 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64
> >
> >
> > i ran sudo -E fs_update as described on
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>
> >
> > but still get the same error
> >
> > Were you guys able to resolve this issue?
> >
> > Thanks so much
> >
> > joseph
> >
> > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladof...@gmail.com
> <mailto:ladof...@gmail.com>
> > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>> wrote:
> >
> > yes, I have the /Applications/freesurfer/lib/gcc
> > directory.(actually, ‘had’ as I reinstalled 5.3)   I installed 6.0
> >     on top of 5.3 without uninstalling 5.3 first, so it was not a clean
> > install.  I will try a clean re-install with the tar file with the
> > steps you suggest. Thanks.
> >
> > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> > From: zkauf...@nmr.mgh.harvard.edu
> <mailto:zkauf...@nmr.mgh.harvard.edu>
> <mailto:zkauf...@nmr.mgh.harvard.edu
> <mailto:zkauf...@nmr.mgh.harvard.edu>>
> > Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Cc: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> >
> >
>  <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
> >
>  <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> 
> <mailto:62233.174.63.82.222.148877

Re: [Freesurfer] mri_vol2surf error in FS6

[VA Research]

I will try to disable SIP

(although i dont want to restart the system because i am curious if this XL
defect will ever be corrected running 80 plus hours now... lol)

attached is the trac -all.log

On Tue, Mar 28, 2017 at 12:40 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote:

> This error is related a new security feature implemented in OS X El
> Capitan:
>
>https://support.apple.com/en-gb/HT204899
>
> You should not be getting this error with version FS6.0, but if you are
> you can always get around it by disabling SIP:
>
>
> http://osxdaily.com/2015/10/05/disable-rootless-system-
> integrity-protection-mac-os-x/
>
> However, I am still curious how/why you are getting this error. Is there
> a trac-all .log file somewhere you can send me so I can see at what
> point exactly this error occurs?
>
> -Zeke
>
>
>
> On 03/28/2017 03:29 PM, VA Research wrote:
> > Hello,
> >
> > i am on el capitan 10.11.6 ,  XQuartz 2.7.8
> >
> > I named the old Applictions/freesurfer directory something else and
> > installed freesurfer 6.0 and sourced through the script, i also changed
> > the subject directory
> >
> > but otherwise i think this is a clean install of FS 6.0
> >
> >
> >  I am running trac-all -prep
> >
> > and am getting the same error
> >
> > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> >
> > dyld: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> >
> > Trace/BPT trap
> > ERROR: input file must be in NIfTI format
> > Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan  9
> > 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64
> >
> >
> > i ran sudo -E fs_update as described on
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> >
> > but still get the same error
> >
> > Were you guys able to resolve this issue?
> >
> > Thanks so much
> >
> > joseph
> >
> > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladof...@gmail.com
> > <mailto:ladof...@gmail.com>> wrote:
> >
> > yes, I have the /Applications/freesurfer/lib/gcc
> > directory.(actually, ‘had’ as I reinstalled 5.3)   I installed 6.0
> > on top of 5.3 without uninstalling 5.3 first, so it was not a clean
> > install.  I will try a clean re-install with the tar file with the
> > steps you suggest. Thanks.
> >
> > Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> > From: zkauf...@nmr.mgh.harvard.edu <mailto:zkauf...@nmr.mgh.
> harvard.edu>
> > Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Cc: freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > Message-ID:
> >
> > <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.
> mgh.harvard.edu>>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Hello Fred,
> >
> > Do you have the /Applications/freesurfer/lib/gcc directory? Also,
> out of
> > curiosity, did freesurfer 5.3 exist on your system before installed
> 6.0?
> > That error shouldnt happen if FS6 is cleanly installed and definitely
> > shouldnt happen of SIPS is disabled.
> >
> > I suppose as a last resort could you just completely remove FS from
> your
> > machine and just install it directly from the tar file (save the
> > license.txt file):
> >
> >  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
> freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
> > <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
> freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz>
> >
> >  $> cp /Applications/freesurfer/license.txt ~
> >  $> sudo rm -rf /Applications/freesurfer
> >  $> sudo tar -C /Applications -xzvf
> > freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
> >  $> sudo mv ~/license.txt /Applications/freesurfer/
> >
> >
> > > Dear FreeSurfer Experts,
> > >   I just installed FS6 and encountered

Re: [Freesurfer] mri_vol2surf error in FS6

[Z K]

This error is related a new security feature implemented in OS X El Capitan:

   https://support.apple.com/en-gb/HT204899

You should not be getting this error with version FS6.0, but if you are 
you can always get around it by disabling SIP:

 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

However, I am still curious how/why you are getting this error. Is there 
a trac-all .log file somewhere you can send me so I can see at what 
point exactly this error occurs?

-Zeke



On 03/28/2017 03:29 PM, VA Research wrote:
> Hello,
>
> i am on el capitan 10.11.6 ,  XQuartz 2.7.8
>
> I named the old Applictions/freesurfer directory something else and
> installed freesurfer 6.0 and sourced through the script, i also changed
> the subject directory
>
> but otherwise i think this is a clean install of FS 6.0
>
>
>  I am running trac-all -prep
>
> and am getting the same error
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Trace/BPT trap
> ERROR: input file must be in NIfTI format
> Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan  9
> 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64
>
>
> i ran sudo -E fs_update as described on
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
>
> but still get the same error
>
> Were you guys able to resolve this issue?
>
> Thanks so much
>
> joseph
>
> On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladof...@gmail.com
> <mailto:ladof...@gmail.com>> wrote:
>
> yes, I have the /Applications/freesurfer/lib/gcc
> directory.(actually, ‘had’ as I reinstalled 5.3)   I installed 6.0
> on top of 5.3 without uninstalling 5.3 first, so it was not a clean
> install.  I will try a clean re-install with the tar file with the
> steps you suggest. Thanks.
>
>     Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> From: zkauf...@nmr.mgh.harvard.edu <mailto:zkauf...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Cc: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
>
> <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu
> <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello Fred,
>
> Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
> curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
> That error shouldnt happen if FS6 is cleanly installed and definitely
> shouldnt happen of SIPS is disabled.
>
> I suppose as a last resort could you just completely remove FS from your
> machine and just install it directly from the tar file (save the
> license.txt file):
>
>  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
> 
> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz>
>
>  $> cp /Applications/freesurfer/license.txt ~
>  $> sudo rm -rf /Applications/freesurfer
>  $> sudo tar -C /Applications -xzvf
> freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
>  $> sudo mv ~/license.txt /Applications/freesurfer/
>
>
> > Dear FreeSurfer Experts,
> >   I just installed FS6 and encountered the following error, which I 
> can
> > replicate by just entering ???mri_vol2surf??? on the command line:
> >
> > /Users/fred 3> mri_vol2surf
> > dyld: lazy symbol binding failed: Symbol not found:
> ___emutls_get_address
> >  Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >  Expected in: /usr/lib/libSystem.B.dylib
> >
> > dyld: Symbol not found: ___emutls_get_address
> >  Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >  Expected in: /usr/lib/libSystem.B.dylib
> >
> > I am running Mac OS X El Capital 10.11.6, after searching the
> archives I
> > also tried turning off SIP, which did not help.  Any  o

Re: [Freesurfer] mri_vol2surf error in FS6

[VA Research]

Hello,

i am on el capitan 10.11.6 ,  XQuartz 2.7.8

I named the old Applictions/freesurfer directory something else and
installed freesurfer 6.0 and sourced through the script, i also changed the
subject directory

but otherwise i think this is a clean install of FS 6.0


 I am running trac-all -prep

and am getting the same error

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap
ERROR: input file must be in NIfTI format
Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan  9 23:07:29
PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64


i ran sudo -E fs_update as described on
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

but still get the same error

Were you guys able to resolve this issue?

Thanks so much

joseph

On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladof...@gmail.com> wrote:

> yes, I have the /Applications/freesurfer/lib/gcc directory.(actually,
> ‘had’ as I reinstalled 5.3)   I installed 6.0 on top of 5.3 without
> uninstalling 5.3 first, so it was not a clean install.  I will try a clean
> re-install with the tar file with the steps you suggest. Thanks.
>
> Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> From: zkauf...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hello Fred,
>
> Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
> curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
> That error shouldnt happen if FS6 is cleanly installed and definitely
> shouldnt happen of SIPS is disabled.
>
> I suppose as a last resort could you just completely remove FS from your
> machine and just install it directly from the tar file (save the
> license.txt file):
>
>  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
> freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
>
>  $> cp /Applications/freesurfer/license.txt ~
>  $> sudo rm -rf /Applications/freesurfer
>  $> sudo tar -C /Applications -xzvf
> freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
>  $> sudo mv ~/license.txt /Applications/freesurfer/
>
>
> > Dear FreeSurfer Experts,
> >   I just installed FS6 and encountered the following error, which I
> can
> > replicate by just entering ???mri_vol2surf??? on the command line:
> >
> > /Users/fred 3> mri_vol2surf
> > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> >  Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >  Expected in: /usr/lib/libSystem.B.dylib
> >
> > dyld: Symbol not found: ___emutls_get_address
> >  Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >  Expected in: /usr/lib/libSystem.B.dylib
> >
> > I am running Mac OS X El Capital 10.11.6, after searching the archives I
> > also tried turning off SIP, which did not help.  Any  other advice?
> >
> > Thanks,
> > Fred
> >
> >
> > Fred Lado, MD PhD
> > Director, Epilepsy - Central and Eastern Regions
> > Northwell Health
> > 917-608-1881 (mobile)
> > 516-325-7000 (practice)
> > 516-325-7001 (fax)
> > fl...@northwell.edu
> >
> >
> >
> >
> >
> > Confidentiality Notice: This document is protected by EDUCATIONAL LAW
> 6527
> > PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any
> > attachments, is for the sole use of the intended recipient(s) and may
> > contain confidential and privileged information. Any unauthorized review,
> > use, disclosure or distribution is prohibited and may be unlawful. If you
> > are not the intended recipient, please delete this e-mail immediately.
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Thank you very much Douglas,
You made my day !

Have a good day,
Redwan

On 14 March 2017 at 10:48, Douglas Greve  wrote:

> Yes, I see a spot on the medial wall. You can also look at it in the
> volume with
>
> tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay
> multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
>
> On 3/14/17 1:45 PM, Redwan Maatoug wrote:
>
> Hi Bruce,
>
> Yes, I did.
> Do you see something ?
>
> Thank you,
> Redwan
>
> On 14 March 2017 at 09:19, Douglas Greve 
> wrote:
>
>> did you look at the medial wall?
>>
>> On 3/13/17 8:48 PM, Redwan Maatoug wrote:
>>
>> Thank you very much Douglas,
>>
>> I think that I probably miss something.
>> There is no error in the terminal but when i launch tksurfer, I have the
>> following screenshot (screen1). The overlay is loaded but the coordinates
>> are 0.0 and the overlay is not in a different color that the brain.
>> I have attached, in case, the brain file and the volumetric file.
>>
>> As you can see, I have followed all the instructions :
>>
>> 1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
>> MNI152.dat --t1 --init-coreg
>>
>> 2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
>> --hemi lh --o ./multidem.mgh
>>
>> 3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1
>>
>> Thank you,
>> Best,
>>
>> Redwan Maatoug
>> Resident in psychiatry
>> Stanford University
>> Amit Etkin lab
>>
>> On 13 March 2017 at 14:51, Douglas N Greve 
>> wrote:
>>
>>> The file you created is not a label so don't try to load it with -label.
>>> Instead use -overlay file.mgh -fminmax .5 1
>>>
>>>
>>>
>>> On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
>>> > Hi Douglas,
>>> >
>>> > Sorry to bother you, again.
>>> > Actually, my command was t1 and not t2 but even with t1 nothing works.
>>> > So if my command line is exact, do you think it is a problem with my
>>> > files ?
>>> >
>>> > Thank you,
>>> >
>>> > Redwan Maatoug
>>> > Resident in psychiatry
>>> > Stanford University
>>> > Amit Etkin lab
>>> >
>>> > On 13 March 2017 at 13:41, Douglas N Greve >> > > wrote:
>>> >
>>> > Use --t1 (I assume the --tw was supposed to be --t2, which is
>>> > wrong for
>>> > that mni152 volume)
>>> >
>>> >
>>> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
>>> > > Hi Douglas,
>>> > >
>>> > > Indeed you have already helped me !
>>> > > Thank you for your help and for your time.
>>> > >
>>> > > I have tried  to do, as you said.
>>> > > I have used  the brain image for the registration and then I have
>>> > > tried to convert my ROI nifti volumetric file into a surface file
>>> > > using this registration file.
>>> > >
>>> > > I do not know what is wrong with my command line and I tried
>>> > many many
>>> > > things.
>>> > >
>>> > > I have attached two files
>>> > > (MNI152_T1_2mm_brain.nii is the brain file,
>>> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
>>> > >
>>> > > I have tried the following commands :
>>> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
>>> > > MNI152.dat --tw --init-coreg*
>>> > >
>>> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
>>> > > MNI152.dat --hemi lh --o ./multidem.mgh*
>>> > >
>>> > > I do not know if the output format .mgh is correct.
>>> > > Anyway when I launch it with :
>>> > > *tksurfer fsaverage lh inflated -label multidem.mgh*
>>> > >
>>> > > the multidem.mgh file does not appear.
>>> > >
>>> > > Thank you by advance for your advice,
>>> > > Best,
>>> > > Redwan
>>> > >
>>> > > On 9 March 2017 at 09:09, Douglas N Greve
>>> > 
>>> > > >> > >> wrote:
>>> > >
>>> > > didn't I respond to this earlier this week? the images
>>> > appear to be
>>> > > binarized regions of interest and not whole (or ever partial)
>>> > > brain. To
>>> > > run the registration, you will need an actual brain. If you
>>> > > created the
>>> > > ROI from a brain image, then use that image to create the
>>> reg,
>>> > > then run
>>> > > vol2surf using that reg with the ROI as input
>>> > >
>>> > >
>>> > > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
>>> > > > Hi experts,
>>> > > >
>>> > > > I try to convert my volumetric nifti file to surface files.
>>> > > >
>>> > > > My nifti volumetric file looks like : 1. screenshot
>>> > > > I have first registered the volumetric file using
>>> bbregister
>>> > > with this
>>> > > > command line :
>>> > > > *bbregister --s fsaverage 

Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

Yes, I see a spot on the medial wall. You can also look at it in the 
volume with


tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay 
multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat



On 3/14/17 1:45 PM, Redwan Maatoug wrote:

Hi Bruce,

Yes, I did.
Do you see something ?

Thank you,
Redwan

On 14 March 2017 at 09:19, Douglas Greve > wrote:


did you look at the medial wall?


On 3/13/17 8:48 PM, Redwan Maatoug wrote:

Thank you very much Douglas,

I think that I probably miss something.
There is no error in the terminal but when i launch tksurfer, I
have the following screenshot (screen1). The overlay is loaded
but the coordinates are 0.0 and the overlay is not in a
different color that the brain.
I have attached, in case, the brain file and the volumetric file.

As you can see, I have followed all the instructions :

1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
MNI152.dat --t1 --init-coreg

2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
MNI152.dat --hemi lh --o ./multidem.mgh

3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1

Thank you,
Best,

Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab

On 13 March 2017 at 14:51, Douglas N Greve
> wrote:

The file you created is not a label so don't try to load it
with -label.
Instead use -overlay file.mgh -fminmax .5 1



On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Sorry to bother you, again.
> Actually, my command was t1 and not t2 but even with t1
nothing works.
> So if my command line is exact, do you think it is a
problem with my
> files ?
>
> Thank you,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 13:41, Douglas N Greve

> >> wrote:
>
> Use --t1 (I assume the --tw was supposed to be --t2,
which is
> wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and
then I have
> > tried to convert my ROI nifti volumetric file into a
surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and
I tried
> many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov
MNI152_T1_2mm_brain.nii --reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov
multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve
> 
>
> > 
> >
> > didn't I respond to this earlier this week? the
images
> appear to be
> > binarized regions of interest and not whole (or
ever partial)
> > brain. To
> > run the registration, you will need an actual
brain. If you
> > created the
> > ROI from a brain image, then use that image to
create the reg,
> > then 

Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Bruce,

Yes, I did.
Do you see something ?

Thank you,
Redwan

On 14 March 2017 at 09:19, Douglas Greve  wrote:

> did you look at the medial wall?
>
> On 3/13/17 8:48 PM, Redwan Maatoug wrote:
>
> Thank you very much Douglas,
>
> I think that I probably miss something.
> There is no error in the terminal but when i launch tksurfer, I have the
> following screenshot (screen1). The overlay is loaded but the coordinates
> are 0.0 and the overlay is not in a different color that the brain.
> I have attached, in case, the brain file and the volumetric file.
>
> As you can see, I have followed all the instructions :
>
> 1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152.dat
> --t1 --init-coreg
>
> 2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
> --hemi lh --o ./multidem.mgh
>
> 3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1
>
> Thank you,
> Best,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 14:51, Douglas N Greve 
> wrote:
>
>> The file you created is not a label so don't try to load it with -label.
>> Instead use -overlay file.mgh -fminmax .5 1
>>
>>
>>
>> On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
>> > Hi Douglas,
>> >
>> > Sorry to bother you, again.
>> > Actually, my command was t1 and not t2 but even with t1 nothing works.
>> > So if my command line is exact, do you think it is a problem with my
>> > files ?
>> >
>> > Thank you,
>> >
>> > Redwan Maatoug
>> > Resident in psychiatry
>> > Stanford University
>> > Amit Etkin lab
>> >
>> > On 13 March 2017 at 13:41, Douglas N Greve > > > wrote:
>> >
>> > Use --t1 (I assume the --tw was supposed to be --t2, which is
>> > wrong for
>> > that mni152 volume)
>> >
>> >
>> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
>> > > Hi Douglas,
>> > >
>> > > Indeed you have already helped me !
>> > > Thank you for your help and for your time.
>> > >
>> > > I have tried  to do, as you said.
>> > > I have used  the brain image for the registration and then I have
>> > > tried to convert my ROI nifti volumetric file into a surface file
>> > > using this registration file.
>> > >
>> > > I do not know what is wrong with my command line and I tried
>> > many many
>> > > things.
>> > >
>> > > I have attached two files
>> > > (MNI152_T1_2mm_brain.nii is the brain file,
>> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
>> > >
>> > > I have tried the following commands :
>> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
>> > > MNI152.dat --tw --init-coreg*
>> > >
>> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
>> > > MNI152.dat --hemi lh --o ./multidem.mgh*
>> > >
>> > > I do not know if the output format .mgh is correct.
>> > > Anyway when I launch it with :
>> > > *tksurfer fsaverage lh inflated -label multidem.mgh*
>> > >
>> > > the multidem.mgh file does not appear.
>> > >
>> > > Thank you by advance for your advice,
>> > > Best,
>> > > Redwan
>> > >
>> > > On 9 March 2017 at 09:09, Douglas N Greve
>> > 
>> > > > > >> wrote:
>> > >
>> > > didn't I respond to this earlier this week? the images
>> > appear to be
>> > > binarized regions of interest and not whole (or ever partial)
>> > > brain. To
>> > > run the registration, you will need an actual brain. If you
>> > > created the
>> > > ROI from a brain image, then use that image to create the reg,
>> > > then run
>> > > vol2surf using that reg with the ROI as input
>> > >
>> > >
>> > > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
>> > > > Hi experts,
>> > > >
>> > > > I try to convert my volumetric nifti file to surface files.
>> > > >
>> > > > My nifti volumetric file looks like : 1. screenshot
>> > > > I have first registered the volumetric file using bbregister
>> > > with this
>> > > > command line :
>> > > > *bbregister --s fsaverage --mov segment_7.nii --reg
>> > > segment_7.dat --t1
>> > > > --init-coreg*
>> > > >
>> > > > then I have used the following command line and the file
>> > looks like
>> > > > screenshot 1 attached :
>> > > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
>> > > >
>> > > > And after that, I have tried to convert my volumetric file
>> to
>> > > surface
>> > > > file with this command line :
>> > > >
>> > > > *mri_vol2surf --src 

Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

did you look at the medial wall?


On 3/13/17 8:48 PM, Redwan Maatoug wrote:

Thank you very much Douglas,

I think that I probably miss something.
There is no error in the terminal but when i launch tksurfer, I have 
the following screenshot (screen1). The overlay is loaded but the 
coordinates are 0.0 and the overlay is not in a different color 
that the brain.

I have attached, in case, the brain file and the volumetric file.

As you can see, I have followed all the instructions :

1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg 
MNI152.dat --t1 --init-coreg


2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat 
--hemi lh --o ./multidem.mgh


3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1

Thank you,
Best,

Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab

On 13 March 2017 at 14:51, Douglas N Greve > wrote:


The file you created is not a label so don't try to load it with
-label.
Instead use -overlay file.mgh -fminmax .5 1



On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Sorry to bother you, again.
> Actually, my command was t1 and not t2 but even with t1 nothing
works.
> So if my command line is exact, do you think it is a problem with my
> files ?
>
> Thank you,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 13:41, Douglas N Greve

> >> wrote:
>
> Use --t1 (I assume the --tw was supposed to be --t2, which is
> wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and then
I have
> > tried to convert my ROI nifti volumetric file into a
surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried
> many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii
--reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve
> 
>
> > 
> >
> > didn't I respond to this earlier this week? the images
> appear to be
> > binarized regions of interest and not whole (or ever
partial)
> > brain. To
> > run the registration, you will need an actual brain.
If you
> > created the
> > ROI from a brain image, then use that image to create
the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface
files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using
bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file
> looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat
--surf*
> >  

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

The file you created is not a label so don't try to load it with -label. 
Instead use -overlay file.mgh -fminmax .5 1



On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Sorry to bother you, again.
> Actually, my command was t1 and not t2 but even with t1 nothing works.
> So if my command line is exact, do you think it is a problem with my 
> files ?
>
> Thank you,
>
> Redwan Maatoug
> Resident in psychiatry
> Stanford University
> Amit Etkin lab
>
> On 13 March 2017 at 13:41, Douglas N Greve  > wrote:
>
> Use --t1 (I assume the --tw was supposed to be --t2, which is
> wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and then I have
> > tried to convert my ROI nifti volumetric file into a surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried
> many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve
> 
> >  >> wrote:
> >
> > didn't I respond to this earlier this week? the images
> appear to be
> > binarized regions of interest and not whole (or ever partial)
> > brain. To
> > run the registration, you will need an actual brain. If you
> > created the
> > ROI from a brain image, then use that image to create the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file
> looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> > >
> > > And after that, I have tried to convert my volumetric file to
> > surface
> > > file with this command line :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.nii --float2int round*
> > >
> > > But with this command when I load the file with freeview
> it does not
> > > work and with tkregister the file is empty.
> > >
> > > Or this one :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> --hemi
> > lh --o
> > > ./segment_7-lh.w --out_type paint --float2int tkregister*
> > >
> > > But with this command I have this warning :
> > > Warning: all vertex values are zero
> > >
> > > Could you please help me to convert my volumetric files
> because I am
> > > probably doing someting wrong. All my files come from an
> Atlas and I
> > > just need to convert them to surfaces files.
> > >
> > > Thank you for your help,
> > > Redwan
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 

Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Douglas,

Sorry to bother you, again.
Actually, my command was t1 and not t2 but even with t1 nothing works.
So if my command line is exact, do you think it is a problem with my files ?

Thank you,

Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab

On 13 March 2017 at 13:41, Douglas N Greve 
wrote:

> Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for
> that mni152 volume)
>
>
> On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Indeed you have already helped me !
> > Thank you for your help and for your time.
> >
> > I have tried  to do, as you said.
> > I have used  the brain image for the registration and then I have
> > tried to convert my ROI nifti volumetric file into a surface file
> > using this registration file.
> >
> > I do not know what is wrong with my command line and I tried many many
> > things.
> >
> > I have attached two files
> > (MNI152_T1_2mm_brain.nii is the brain file,
> > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> >
> > I have tried the following commands :
> > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
> > MNI152.dat --tw --init-coreg*
> >
> > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > MNI152.dat --hemi lh --o ./multidem.mgh*
> >
> > I do not know if the output format .mgh is correct.
> > Anyway when I launch it with :
> > *tksurfer fsaverage lh inflated -label multidem.mgh*
> >
> > the multidem.mgh file does not appear.
> >
> > Thank you by advance for your advice,
> > Best,
> > Redwan
> >
> > On 9 March 2017 at 09:09, Douglas N Greve  > > wrote:
> >
> > didn't I respond to this earlier this week? the images appear to be
> > binarized regions of interest and not whole (or ever partial)
> > brain. To
> > run the registration, you will need an actual brain. If you
> > created the
> > ROI from a brain image, then use that image to create the reg,
> > then run
> > vol2surf using that reg with the ROI as input
> >
> >
> > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > Hi experts,
> > >
> > > I try to convert my volumetric nifti file to surface files.
> > >
> > > My nifti volumetric file looks like : 1. screenshot
> > > I have first registered the volumetric file using bbregister
> > with this
> > > command line :
> > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > segment_7.dat --t1
> > > --init-coreg*
> > >
> > > then I have used the following command line and the file looks like
> > > screenshot 1 attached :
> > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> > >
> > > And after that, I have tried to convert my volumetric file to
> > surface
> > > file with this command line :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> > lh --o
> > > ./segment_7-lh.nii --float2int round*
> > >
> > > But with this command when I load the file with freeview it does
> not
> > > work and with tkregister the file is empty.
> > >
> > > Or this one :
> > >
> > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> > lh --o
> > > ./segment_7-lh.w --out_type paint --float2int tkregister*
> > >
> > > But with this command I have this warning :
> > > Warning: all vertex values are zero
> > >
> > > Could you please help me to convert my volumetric files because I
> am
> > > probably doing someting wrong. All my files come from an Atlas and
> I
> > > just need to convert them to surfaces files.
> > >
> > > Thank you for your help,
> > > Redwan
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > 
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > 
> >
> > ___
> > Freesurfer mailing list
> > 

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for 
that mni152 volume)


On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Indeed you have already helped me !
> Thank you for your help and for your time.
>
> I have tried  to do, as you said.
> I have used  the brain image for the registration and then I have 
> tried to convert my ROI nifti volumetric file into a surface file 
> using this registration file.
>
> I do not know what is wrong with my command line and I tried many many 
> things.
>
> I have attached two files
> (MNI152_T1_2mm_brain.nii is the brain file, 
> multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
>
> I have tried the following commands :
> 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg 
> MNI152.dat --tw --init-coreg*
>
> 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg 
> MNI152.dat --hemi lh --o ./multidem.mgh*
>
> I do not know if the output format .mgh is correct.
> Anyway when I launch it with :
> *tksurfer fsaverage lh inflated -label multidem.mgh*
>
> the multidem.mgh file does not appear.
>
> Thank you by advance for your advice,
> Best,
> Redwan
>
> On 9 March 2017 at 09:09, Douglas N Greve  > wrote:
>
> didn't I respond to this earlier this week? the images appear to be
> binarized regions of interest and not whole (or ever partial)
> brain. To
> run the registration, you will need an actual brain. If you
> created the
> ROI from a brain image, then use that image to create the reg,
> then run
> vol2surf using that reg with the ROI as input
>
>
> On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > Hi experts,
> >
> > I try to convert my volumetric nifti file to surface files.
> >
> > My nifti volumetric file looks like : 1. screenshot
> > I have first registered the volumetric file using bbregister
> with this
> > command line :
> > *bbregister --s fsaverage --mov segment_7.nii --reg
> segment_7.dat --t1
> > --init-coreg*
> >
> > then I have used the following command line and the file looks like
> > screenshot 1 attached :
> > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> >
> > And after that, I have tried to convert my volumetric file to
> surface
> > file with this command line :
> >
> > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> lh --o
> > ./segment_7-lh.nii --float2int round*
> >
> > But with this command when I load the file with freeview it does not
> > work and with tkregister the file is empty.
> >
> > Or this one :
> >
> > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi
> lh --o
> > ./segment_7-lh.w --out_type paint --float2int tkregister*
> >
> > But with this command I have this warning :
> > Warning: all vertex values are zero
> >
> > Could you please help me to convert my volumetric files because I am
> > probably doing someting wrong. All my files come from an Atlas and I
> > just need to convert them to surfaces files.
> >
> > Thank you for your help,
> > Redwan
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in 

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

didn't I respond to this earlier this week? the images appear to be 
binarized regions of interest and not whole (or ever partial) brain. To 
run the registration, you will need an actual brain. If you created the 
ROI from a brain image, then use that image to create the reg, then run 
vol2surf using that reg with the ROI as input


On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> Hi experts,
>
> I try to convert my volumetric nifti file to surface files.
>
> My nifti volumetric file looks like : 1. screenshot
> I have first registered the volumetric file using bbregister with this 
> command line :
> *bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1 
> --init-coreg*
>
> then I have used the following command line and the file looks like 
> screenshot 1 attached :
> *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
>
> And after that, I have tried to convert my volumetric file to surface 
> file with this command line :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.nii --float2int round*
>
> But with this command when I load the file with freeview it does not 
> work and with tkregister the file is empty.
>
> Or this one :
>
> *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.w --out_type paint --float2int tkregister*
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Could you please help me to convert my volumetric files because I am 
> probably doing someting wrong. All my files come from an Atlas and I 
> just need to convert them to surfaces files.
>
> Thank you for your help,
> Redwan
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

What is that input file? It looks like a mask of some part of the brain


On 03/03/2017 06:14 PM, Redwan Maatoug wrote:
> Hi Douglas,
>
> Thank you for your help,
>
> So I still can't convert my volumetric file to a surface file and I 
> don't know what I am doing wrong.
>
> My nifti volumetric file looks like : 1. screenshot
> As you said, i have first registered the volumetric file
>  using bbregister.
>  I have used this command line :
> tkregister2 --mov segment_7.nii --reg register7.dat --surf
>  (knowing that segment_7.nii is my volumetric file which looks like 
> 1.screenshot).
> With this command line, my output is this file : 2.screenshot (attached).
>
> Am I satisfied with this file ? if not what can I do to improve the 
> result and the matching ?
>
> And after that, I have tried to convert my volumetric file to surface 
> file with this command line :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.nii --float2int round
>
> But with this command when I load the file with freeview it does not 
> work and with tkregister the file is empty.
>
> Or this one :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o 
> ./segment_7-lh.w --out_type paint --float2int tkregister
>
> But with this command I have the following warning :
> Warning: all vertex values are zero
>
> Thank you by advance for your precious help,
> Have a nice day,
> Redwan
>
>
> On 2 March 2017 at 10:07, Redwan Maatoug  > wrote:
>
> Hi Douglas,
>
> Thank you for your help,
>
> So I still can't convert my volumetric file to a surface file and
> I don't know what I am doing wrong.
>
> My nifti volumetric file looks like : 1. screenshot
> As you said, i have first registered the volumetric file
>  using bbregister.
>  I have used this command line :
> tkregister2 --mov segment_7.nii --reg register7.dat --surf
>  (knowing that segment_7.nii is my volumetric file which looks
> like 1.screenshot).
> With this command line, my output is this file : 2.screenshot
> (attached).
>
> Am I satisfied with this file ? if not what can I do to improve
> the result and the matching ?
>
> And after that, I have tried to convert my volumetric file to
> surface file with this command line :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh
> --o ./segment_7-lh.nii --float2int round
>
> But with this command when I load the file with freeview it does
> not work and with tkregister the file is empty.
>
> Or this one :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh
> --o ./segment_7-lh.w --out_type paint --float2int tkregister
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Thank you by advance for your precious help,
> Have a nice day,
> Redwan
>
> On 1 March 2017 at 07:31, Douglas Greve  > wrote:
>
> Hi Redwan,
>
> You'll need to register your volume to an FS-analyzed data set
> (probably using bbregister). Then apply mri_vol2surf (run with
> --help to get examples)
>
> doug
>
>
> On 2/28/17 5:17 PM, Redwan Maatoug wrote:
>> Hi all !
>>
>> I would like to convert my files : volumetrics nifti files to
>> surfaces files.
>> My volumetrics nifti files come from an Atlas and I would
>> like to convert them to surfaces files (i need the surfaces
>> files).
>>
>> Could you please tell me the process because I have tried
>> many things like :
>>
>> mri_vol2surf --src pathwaytomyfile --hemi lh --float2int
>> round --out thepathwayIwantToputmySurfaceFileAfterConversion
>>
>> And it did not work.
>>
>> Thank you for your help,
>> Redwan
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
> ___ Freesurfer
> mailing list Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> The information in this e-mail is intended only for the person
> to whom it is addressed. If you believe this e-mail was sent
> to you in error and the e-mail contains patient information,
> please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline
> 

Re: [Freesurfer] mri_vol2surf error in FS6

[Fred Lado]

yes, I have the /Applications/freesurfer/lib/gcc directory.(actually, ‘had’ as 
I reinstalled 5.3)   I installed 6.0 on top of 5.3 without uninstalling 5.3 
first, so it was not a clean install.  I will try a clean re-install with the 
tar file with the steps you suggest. Thanks. 

Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
From: zkauf...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf error in FS6
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

Hello Fred,

Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
That error shouldnt happen if FS6 is cleanly installed and definitely
shouldnt happen of SIPS is disabled.

I suppose as a last resort could you just completely remove FS from your
machine and just install it directly from the tar file (save the
license.txt file):

 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz

 $> cp /Applications/freesurfer/license.txt ~
 $> sudo rm -rf /Applications/freesurfer
 $> sudo tar -C /Applications -xzvf
freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
 $> sudo mv ~/license.txt /Applications/freesurfer/


> Dear FreeSurfer Experts,
>   I just installed FS6 and encountered the following error, which I can
> replicate by just entering ???mri_vol2surf??? on the command line:
> 
> /Users/fred 3> mri_vol2surf
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>  Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>  Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ___emutls_get_address
>  Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>  Expected in: /usr/lib/libSystem.B.dylib
> 
> I am running Mac OS X El Capital 10.11.6, after searching the archives I
> also tried turning off SIP, which did not help.  Any  other advice?
> 
> Thanks,
> Fred
> 
> 
> Fred Lado, MD PhD
> Director, Epilepsy - Central and Eastern Regions
> Northwell Health
> 917-608-1881 (mobile)
> 516-325-7000 (practice)
> 516-325-7001 (fax)
> fl...@northwell.edu
> 
> 
> 
> 
> 
> Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527
> PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized review,
> use, disclosure or distribution is prohibited and may be unlawful. If you
> are not the intended recipient, please delete this e-mail immediately.
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf error in FS6

[zkaufman]

Hello Fred,

Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
That error shouldnt happen if FS6 is cleanly installed and definitely
shouldnt happen of SIPS is disabled.

I suppose as a last resort could you just completely remove FS from your
machine and just install it directly from the tar file (save the
license.txt file):

  
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz

  $> cp /Applications/freesurfer/license.txt ~
  $> sudo rm -rf /Applications/freesurfer
  $> sudo tar -C /Applications -xzvf
freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz
  $> sudo mv ~/license.txt /Applications/freesurfer/


> Dear FreeSurfer Experts,
>   I just installed FS6 and encountered the following error, which I can
> replicate by just entering “mri_vol2surf” on the command line:
>
> /Users/fred 3> mri_vol2surf
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> I am running Mac OS X El Capital 10.11.6, after searching the archives I
> also tried turning off SIP, which did not help.  Any  other advice?
>
> Thanks,
> Fred
>
>
> Fred Lado, MD PhD
> Director, Epilepsy - Central and Eastern Regions
> Northwell Health
> 917-608-1881 (mobile)
> 516-325-7000 (practice)
> 516-325-7001 (fax)
> fl...@northwell.edu
>
>
>
>
>
> Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527
> PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any
> attachments, is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information. Any unauthorized review,
> use, disclosure or distribution is prohibited and may be unlawful. If you
> are not the intended recipient, please delete this e-mail immediately.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and I don't
know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot
As you said, i have first registered the volumetric file
 using bbregister.
 I have used this command line :
tkregister2 --mov segment_7.nii --reg register7.dat --surf
 (knowing that segment_7.nii is my volumetric file which looks like
1.screenshot).
With this command line, my output is this file : 2.screenshot (attached).

Am I satisfied with this file ? if not what can I do to improve the result
and the matching ?

And after that, I have tried to convert my volumetric file to surface file
with this command line :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.nii --float2int round

But with this command when I load the file with freeview it does not work
and with tkregister the file is empty.

Or this one :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.w --out_type paint --float2int tkregister

But with this command I have the following warning :
Warning: all vertex values are zero

Thank you by advance for your precious help,
Have a nice day,
Redwan


On 2 March 2017 at 10:07, Redwan Maatoug  wrote:

> Hi Douglas,
>
> Thank you for your help,
>
> So I still can't convert my volumetric file to a surface file and I don't
> know what I am doing wrong.
>
> My nifti volumetric file looks like : 1. screenshot
> As you said, i have first registered the volumetric file
>  using bbregister.
>  I have used this command line :
> tkregister2 --mov segment_7.nii --reg register7.dat --surf
>  (knowing that segment_7.nii is my volumetric file which looks like
> 1.screenshot).
> With this command line, my output is this file : 2.screenshot (attached).
>
> Am I satisfied with this file ? if not what can I do to improve the result
> and the matching ?
>
> And after that, I have tried to convert my volumetric file to surface file
> with this command line :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.nii --float2int round
>
> But with this command when I load the file with freeview it does not work
> and with tkregister the file is empty.
>
> Or this one :
>
> mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
> ./segment_7-lh.w --out_type paint --float2int tkregister
>
> But with this command I have this warning :
> Warning: all vertex values are zero
>
> Thank you by advance for your precious help,
> Have a nice day,
> Redwan
>
> On 1 March 2017 at 07:31, Douglas Greve  wrote:
>
>> Hi Redwan,
>>
>> You'll need to register your volume to an FS-analyzed data set (probably
>> using bbregister). Then apply mri_vol2surf (run with --help to get examples)
>>
>> doug
>>
>> On 2/28/17 5:17 PM, Redwan Maatoug wrote:
>>
>> Hi all !
>>
>> I would like to convert my files : volumetrics nifti files to surfaces
>> files.
>> My volumetrics nifti files come from an Atlas and I would like to convert
>> them to surfaces files (i need the surfaces files).
>>
>> Could you please tell me the process because I have tried many things
>> like :
>>
>> mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out
>> thepathwayIwantToputmySurfaceFileAfterConversion
>>
>> And it did not work.
>>
>> Thank you for your help,
>> Redwan
>>
>>
>>
>> ___
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>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
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>> properly
>> dispose of the e-mail.
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Re: [Freesurfer] mri_vol2surf

[Redwan Maatoug]

Hi Douglas,

Thank you for your help,

So I still can't convert my volumetric file to a surface file and I don't
know what I am doing wrong.

My nifti volumetric file looks like : 1. screenshot
As you said, i have first registered the volumetric file
 using bbregister.
 I have used this command line :
tkregister2 --mov segment_7.nii --reg register7.dat --surf
 (knowing that segment_7.nii is my volumetric file which looks like
1.screenshot).
With this command line, my output is this file : 2.screenshot (attached).

Am I satisfied with this file ? if not what can I do to improve the result
and the matching ?

And after that, I have tried to convert my volumetric file to surface file
with this command line :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.nii --float2int round

But with this command when I load the file with freeview it does not work
and with tkregister the file is empty.

Or this one :

mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o
./segment_7-lh.w --out_type paint --float2int tkregister

But with this command I have this warning :
Warning: all vertex values are zero

Thank you by advance for your precious help,
Have a nice day,
Redwan

On 1 March 2017 at 07:31, Douglas Greve  wrote:

> Hi Redwan,
>
> You'll need to register your volume to an FS-analyzed data set (probably
> using bbregister). Then apply mri_vol2surf (run with --help to get examples)
>
> doug
>
> On 2/28/17 5:17 PM, Redwan Maatoug wrote:
>
> Hi all !
>
> I would like to convert my files : volumetrics nifti files to surfaces
> files.
> My volumetrics nifti files come from an Atlas and I would like to convert
> them to surfaces files (i need the surfaces files).
>
> Could you please tell me the process because I have tried many things like
> :
>
> mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out
> thepathwayIwantToputmySurfaceFileAfterConversion
>
> And it did not work.
>
> Thank you for your help,
> Redwan
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf

[Douglas Greve]

Hi Redwan,

You'll need to register your volume to an FS-analyzed data set (probably 
using bbregister). Then apply mri_vol2surf (run with --help to get examples)


doug


On 2/28/17 5:17 PM, Redwan Maatoug wrote:

Hi all !

I would like to convert my files : volumetrics nifti files to surfaces 
files.
My volumetrics nifti files come from an Atlas and I would like to 
convert them to surfaces files (i need the surfaces files).


Could you please tell me the process because I have tried many things 
like :


mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out 
thepathwayIwantToputmySurfaceFileAfterConversion


And it did not work.

Thank you for your help,
Redwan



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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] mri_vol2surf

[Zhivago]

That makes life so easy!  Thanks Douglas.

Cheers,
Zhivago...

On Tue, Jan 24, 2017 at 1:03 AM, Douglas N Greve 
wrote:

> Yes. Easiest way it probably in matlab.
>
> Read in a surface overlay to use as a template
>
> overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh');
>
> overlay.vol = yourdata;
> MRIwrite('lh.yourdata.mgh')
>
>
>
> On 01/20/2017 11:13 PM, Zhivago wrote:
> > Hi,
> >
> > If I know the activation values at each vertex/face of a surface, can
> > I create an mgh file independent of mri_vol2surf and overlay it on any
> > other surface or view it independently?
> >
> > Cheers,
> > Zhivago...
> >
> > On Thu, Jan 19, 2017 at 8:28 AM, Zhivago  > > wrote:
> >
> > Thanks a lot, Bruce.
> >
> > Cheers,
> > Zhivago...
> >
> > On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl
> > >
> > wrote:
> >
> > Hi Zhivago
> >
> > tksurfer is deprecated and uses one of the methods available
> > in mri_vol2surf, so our advice would be to use vol2surf
> >
> > cheers
> > Bruce
> > On Wed, 18 Jan 2017, Zhivago wrote:
> >
> > [cleardot.gif]
> >
> > Hi,
> >
> > >From whatever I read, there seem to be 2 ways for
> > overlaying activation maps
> > on surfaces.
> >
> > 1) automatic/manual registration of activation volume to
> > orig.mgz and usage
> > of mri_vol2surf to create the overlay, say ?h.sig.mgh,
> > which can then be
> > overlaid on an inflated surface in freeview or tksurfer
> > using the
> > register.dat.
> >
> > 2) automatic/manual registration of activation volume to
> > orig.mgz and
> > overlay the activation volume on the inflated surface in
> > tksurfer using the
> > register.dat
> >
> > I want to know if both these are valid methods and if so,
> > what are the pros
> > and cons of each.  Seems like mri_vol2surf lets us decide
> > what part of the
> > volume should be projected on the surface using the
> > projfac arguments.  But
> > the direct volume overlay in tksurfer doesn't provide that
> > option.  In that
> > case what part of the volume is projected on to the surface?
> >
> > Thanks,
> > Zhivago...
> >
> > On Sun, Jan 15, 2017 at 10:12 PM, Zhivago
> > > wrote:
> >   Thanks Bruce!  Appreciate all the help,
> >
> > On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
> >  > > wrote:
> >   1) This is up to you. Jon Polimeni had a nice paper
> >   describing the trade-off between accurately
> representing
> >   the local neural response (which is best at the white
> >   border) and statistical power (which is best nearer the
> >   pial surface).
> >
> >   2) This is also up to you.Read the help in
> mri_vol2surf.
> >   e.g.:
> >
> >   mri_vol2surf --help
> >   .
> >   .
> >   .
> >  --projfrac-avg min max del : average along normal
> >
> >   3) it is the way that we support.
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Sun, 15 Jan 2017, Zhivago wrote:
> >
> > Hey Bruce,
> >
> > Thank you very much for the responses!  Had
> > posted a couple of more
> > questions, but looks like it hasn't gone
> > across.  Will really appreciate it
> > if you can provide some answers to these.
> >
> > 1) The mri_vol2surf is used to project the
> > activations from the GM onto an
> > inflated surface, which is usually the
> > inflated smoothwm surface output from
> > reconall.  Will it be more accurate to use the
> > inflated version of the
> > intermediate surface, like halfway between the
> > white and pial matter?  Will
> > it make any kind of sense?
> >
> > 2) When mri_vol2surf projects a volume to a
> > surface, does it average the
> > activation values of voxels along the cortical
> > depth 

Re: [Freesurfer] mri_vol2surf

[Douglas N Greve]

Yes. Easiest way it probably in matlab.

Read in a surface overlay to use as a template

overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh');

overlay.vol = yourdata;
MRIwrite('lh.yourdata.mgh')



On 01/20/2017 11:13 PM, Zhivago wrote:
> Hi,
>
> If I know the activation values at each vertex/face of a surface, can 
> I create an mgh file independent of mri_vol2surf and overlay it on any 
> other surface or view it independently?
>
> Cheers,
> Zhivago...
>
> On Thu, Jan 19, 2017 at 8:28 AM, Zhivago  > wrote:
>
> Thanks a lot, Bruce.
>
> Cheers,
> Zhivago...
>
> On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl
> >
> wrote:
>
> Hi Zhivago
>
> tksurfer is deprecated and uses one of the methods available
> in mri_vol2surf, so our advice would be to use vol2surf
>
> cheers
> Bruce
> On Wed, 18 Jan 2017, Zhivago wrote:
>
> [cleardot.gif]
>
> Hi,
>
> >From whatever I read, there seem to be 2 ways for
> overlaying activation maps
> on surfaces.
>
> 1) automatic/manual registration of activation volume to
> orig.mgz and usage
> of mri_vol2surf to create the overlay, say ?h.sig.mgh,
> which can then be
> overlaid on an inflated surface in freeview or tksurfer
> using the
> register.dat.
>
> 2) automatic/manual registration of activation volume to
> orig.mgz and
> overlay the activation volume on the inflated surface in
> tksurfer using the
> register.dat
>
> I want to know if both these are valid methods and if so,
> what are the pros
> and cons of each.  Seems like mri_vol2surf lets us decide
> what part of the
> volume should be projected on the surface using the
> projfac arguments.  But
> the direct volume overlay in tksurfer doesn't provide that
> option.  In that
> case what part of the volume is projected on to the surface?
>
> Thanks,
> Zhivago...
>
> On Sun, Jan 15, 2017 at 10:12 PM, Zhivago
> > wrote:
>   Thanks Bruce!  Appreciate all the help,
>
> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
>  > wrote:
>   1) This is up to you. Jon Polimeni had a nice paper
>   describing the trade-off between accurately representing
>   the local neural response (which is best at the white
>   border) and statistical power (which is best nearer the
>   pial surface).
>
>   2) This is also up to you.Read the help in mri_vol2surf.
>   e.g.:
>
>   mri_vol2surf --help
>   .
>   .
>   .
>  --projfrac-avg min max del : average along normal
>
>   3) it is the way that we support.
>
>   cheers
>   Bruce
>
>
>   On Sun, 15 Jan 2017, Zhivago wrote:
>
> Hey Bruce,
>
> Thank you very much for the responses!  Had
> posted a couple of more
> questions, but looks like it hasn't gone
> across.  Will really appreciate it
> if you can provide some answers to these.
>
> 1) The mri_vol2surf is used to project the
> activations from the GM onto an
> inflated surface, which is usually the
> inflated smoothwm surface output from
> reconall.  Will it be more accurate to use the
> inflated version of the
> intermediate surface, like halfway between the
> white and pial matter?  Will
> it make any kind of sense?
>
> 2) When mri_vol2surf projects a volume to a
> surface, does it average the
> activation values of voxels along the cortical
> depth or sum it?  What really
> happens beneath?  Any amount of insight will
> be helpful.
>
> 3) Is mri_vol2surf the only way to view
> activation maps on inflated surfaces
> or any surface?
>
> Cheers,
> Zhivago...
>
> 

Re: [Freesurfer] mri_vol2surf

[Zhivago]

Hi,

If I know the activation values at each vertex/face of a surface, can I
create an mgh file independent of mri_vol2surf and overlay it on any other
surface or view it independently?

Cheers,
Zhivago...

On Thu, Jan 19, 2017 at 8:28 AM, Zhivago  wrote:

> Thanks a lot, Bruce.
>
> Cheers,
> Zhivago...
>
> On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl 
> wrote:
>
>> Hi Zhivago
>>
>> tksurfer is deprecated and uses one of the methods available in
>> mri_vol2surf, so our advice would be to use vol2surf
>>
>> cheers
>> Bruce
>> On Wed, 18 Jan 2017, Zhivago wrote:
>>
>> [cleardot.gif]
>>>
>>> Hi,
>>>
>>> From whatever I read, there seem to be 2 ways for overlaying activation
>>> maps
>>> on surfaces.
>>>
>>> 1) automatic/manual registration of activation volume to orig.mgz and
>>> usage
>>> of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be
>>> overlaid on an inflated surface in freeview or tksurfer using the
>>> register.dat.
>>>
>>> 2) automatic/manual registration of activation volume to orig.mgz and
>>> overlay the activation volume on the inflated surface in tksurfer using
>>> the
>>> register.dat
>>>
>>> I want to know if both these are valid methods and if so, what are the
>>> pros
>>> and cons of each.  Seems like mri_vol2surf lets us decide what part of
>>> the
>>> volume should be projected on the surface using the projfac arguments.
>>> But
>>> the direct volume overlay in tksurfer doesn't provide that option.  In
>>> that
>>> case what part of the volume is projected on to the surface?
>>>
>>> Thanks,
>>> Zhivago...
>>>
>>> On Sun, Jan 15, 2017 at 10:12 PM, Zhivago  wrote:
>>>   Thanks Bruce!  Appreciate all the help,
>>>
>>> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
>>>  wrote:
>>>   1) This is up to you. Jon Polimeni had a nice paper
>>>   describing the trade-off between accurately representing
>>>   the local neural response (which is best at the white
>>>   border) and statistical power (which is best nearer the
>>>   pial surface).
>>>
>>>   2) This is also up to you.Read the help in mri_vol2surf.
>>>   e.g.:
>>>
>>>   mri_vol2surf --help
>>>   .
>>>   .
>>>   .
>>>  --projfrac-avg min max del : average along normal
>>>
>>>   3) it is the way that we support.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>>
>>> Hey Bruce,
>>>
>>> Thank you very much for the responses!  Had
>>> posted a couple of more
>>> questions, but looks like it hasn't gone
>>> across.  Will really appreciate it
>>> if you can provide some answers to these.
>>>
>>> 1) The mri_vol2surf is used to project the
>>> activations from the GM onto an
>>> inflated surface, which is usually the
>>> inflated smoothwm surface output from
>>> reconall.  Will it be more accurate to use the
>>> inflated version of the
>>> intermediate surface, like halfway between the
>>> white and pial matter?  Will
>>> it make any kind of sense?
>>>
>>> 2) When mri_vol2surf projects a volume to a
>>> surface, does it average the
>>> activation values of voxels along the cortical
>>> depth or sum it?  What really
>>> happens beneath?  Any amount of insight will
>>> be helpful.
>>>
>>> 3) Is mri_vol2surf the only way to view
>>> activation maps on inflated surfaces
>>> or any surface?
>>>
>>> Cheers,
>>> Zhivago...
>>>
>>> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl
>>> 
>>> wrote:
>>>   Hi Zhivago
>>>
>>>   1) You can project from inside the
>>> ?h.white surface if
>>>   projfrac<0 and outside pial if
>>> projfrac>1. <<0 and >>1 won't
>>>   make much sense though as it starts to
>>> get arbitrary.
>>>
>>>   2) The default projfrac, as documented
>>> in the -help response, is
>>>   0.
>>>
>>>   3) Yes, 0-->white matter boundary. 1-->
>>> pial boundary.
>>>
>>>   4) The .mgh/.mgz file create by vol2surf
>>> is an nvertices x 1 x 1
>>>   vector, which is a scalar field over the
>>> surface.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>
>>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>>
>>> Hi,
>>>
>>>
>>> I do not have a good understanding
>>> of the
>>> mri_vol2surf command.
>>>
>>> 1) Can 

Re: [Freesurfer] mri_vol2surf

[Zhivago]

Thanks a lot, Bruce.

Cheers,
Zhivago...

On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl 
wrote:

> Hi Zhivago
>
> tksurfer is deprecated and uses one of the methods available in
> mri_vol2surf, so our advice would be to use vol2surf
>
> cheers
> Bruce
> On Wed, 18 Jan 2017, Zhivago wrote:
>
> [cleardot.gif]
>>
>> Hi,
>>
>> From whatever I read, there seem to be 2 ways for overlaying activation
>> maps
>> on surfaces.
>>
>> 1) automatic/manual registration of activation volume to orig.mgz and
>> usage
>> of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be
>> overlaid on an inflated surface in freeview or tksurfer using the
>> register.dat.
>>
>> 2) automatic/manual registration of activation volume to orig.mgz and
>> overlay the activation volume on the inflated surface in tksurfer using
>> the
>> register.dat
>>
>> I want to know if both these are valid methods and if so, what are the
>> pros
>> and cons of each.  Seems like mri_vol2surf lets us decide what part of the
>> volume should be projected on the surface using the projfac arguments.
>> But
>> the direct volume overlay in tksurfer doesn't provide that option.  In
>> that
>> case what part of the volume is projected on to the surface?
>>
>> Thanks,
>> Zhivago...
>>
>> On Sun, Jan 15, 2017 at 10:12 PM, Zhivago  wrote:
>>   Thanks Bruce!  Appreciate all the help,
>>
>> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
>>  wrote:
>>   1) This is up to you. Jon Polimeni had a nice paper
>>   describing the trade-off between accurately representing
>>   the local neural response (which is best at the white
>>   border) and statistical power (which is best nearer the
>>   pial surface).
>>
>>   2) This is also up to you.Read the help in mri_vol2surf.
>>   e.g.:
>>
>>   mri_vol2surf --help
>>   .
>>   .
>>   .
>>  --projfrac-avg min max del : average along normal
>>
>>   3) it is the way that we support.
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>
>> Hey Bruce,
>>
>> Thank you very much for the responses!  Had
>> posted a couple of more
>> questions, but looks like it hasn't gone
>> across.  Will really appreciate it
>> if you can provide some answers to these.
>>
>> 1) The mri_vol2surf is used to project the
>> activations from the GM onto an
>> inflated surface, which is usually the
>> inflated smoothwm surface output from
>> reconall.  Will it be more accurate to use the
>> inflated version of the
>> intermediate surface, like halfway between the
>> white and pial matter?  Will
>> it make any kind of sense?
>>
>> 2) When mri_vol2surf projects a volume to a
>> surface, does it average the
>> activation values of voxels along the cortical
>> depth or sum it?  What really
>> happens beneath?  Any amount of insight will
>> be helpful.
>>
>> 3) Is mri_vol2surf the only way to view
>> activation maps on inflated surfaces
>> or any surface?
>>
>> Cheers,
>> Zhivago...
>>
>> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl
>> 
>> wrote:
>>   Hi Zhivago
>>
>>   1) You can project from inside the
>> ?h.white surface if
>>   projfrac<0 and outside pial if
>> projfrac>1. <<0 and >>1 won't
>>   make much sense though as it starts to
>> get arbitrary.
>>
>>   2) The default projfrac, as documented
>> in the -help response, is
>>   0.
>>
>>   3) Yes, 0-->white matter boundary. 1-->
>> pial boundary.
>>
>>   4) The .mgh/.mgz file create by vol2surf
>> is an nvertices x 1 x 1
>>   vector, which is a scalar field over the
>> surface.
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>
>> Hi,
>>
>>
>> I do not have a good understanding
>> of the
>> mri_vol2surf command.
>>
>> 1) Can this only project the part
>> of the volume that
>> lies between the white
>> & pial matter?
>> 2) What is the default projection
>> parameter that it
>> uses?
>> 3) Does projection always start
>> from the white
>> matter, i.e. is 0 the white
>>

Re: [Freesurfer] mri_vol2surf

[Bruce Fischl]

Hi Zhivago

tksurfer is deprecated and uses one of the methods available in 
mri_vol2surf, so our advice would be to use vol2surf


cheers
Bruce
On Wed, 18 Jan 2017, 
Zhivago wrote:



[cleardot.gif]
Hi,

From whatever I read, there seem to be 2 ways for overlaying activation maps
on surfaces.

1) automatic/manual registration of activation volume to orig.mgz and usage
of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be
overlaid on an inflated surface in freeview or tksurfer using the
register.dat.

2) automatic/manual registration of activation volume to orig.mgz and
overlay the activation volume on the inflated surface in tksurfer using the
register.dat

I want to know if both these are valid methods and if so, what are the pros
and cons of each.  Seems like mri_vol2surf lets us decide what part of the
volume should be projected on the surface using the projfac arguments.  But
the direct volume overlay in tksurfer doesn't provide that option.  In that
case what part of the volume is projected on to the surface?

Thanks,
Zhivago...

On Sun, Jan 15, 2017 at 10:12 PM, Zhivago  wrote:
  Thanks Bruce!  Appreciate all the help,

On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
 wrote:
  1) This is up to you. Jon Polimeni had a nice paper
  describing the trade-off between accurately representing
  the local neural response (which is best at the white
  border) and statistical power (which is best nearer the
  pial surface).

  2) This is also up to you.Read the help in mri_vol2surf.
  e.g.:

  mri_vol2surf --help
  .
  .
  .
     --projfrac-avg min max del : average along normal

  3) it is the way that we support.

  cheers
  Bruce


  On Sun, 15 Jan 2017, Zhivago wrote:

Hey Bruce,

Thank you very much for the responses!  Had
posted a couple of more
questions, but looks like it hasn't gone
across.  Will really appreciate it
if you can provide some answers to these.

1) The mri_vol2surf is used to project the
activations from the GM onto an
inflated surface, which is usually the
inflated smoothwm surface output from
reconall.  Will it be more accurate to use the
inflated version of the
intermediate surface, like halfway between the
white and pial matter?  Will
it make any kind of sense?

2) When mri_vol2surf projects a volume to a
surface, does it average the
activation values of voxels along the cortical
depth or sum it?  What really
happens beneath?  Any amount of insight will
be helpful.

3) Is mri_vol2surf the only way to view
activation maps on inflated surfaces
or any surface?

Cheers,
Zhivago...

On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl

wrote:
      Hi Zhivago

      1) You can project from inside the
?h.white surface if
      projfrac<0 and outside pial if
projfrac>1. <<0 and >>1 won't
      make much sense though as it starts to
get arbitrary.

      2) The default projfrac, as documented
in the -help response, is
      0.

      3) Yes, 0-->white matter boundary. 1-->
pial boundary.

      4) The .mgh/.mgz file create by vol2surf
is an nvertices x 1 x 1
      vector, which is a scalar field over the
surface.

      cheers
      Bruce



      On Sun, 15 Jan 2017, Zhivago wrote:

            Hi,


            I do not have a good understanding
of the
            mri_vol2surf command.

            1) Can this only project the part
of the volume that
            lies between the white
            & pial matter?
            2) What is the default projection
parameter that it
            uses?
            3) Does projection always start
from the white
            matter, i.e. is 0 the white
            matter surface?
            4) What is the nature of the mgh
file that is
            created by:
            mri_vol2surf --src
mri/spmT_0002.img --regheader
            s04  --interp nearest
            --hemi lh --o lh.sig.mgh

            Thanks,
            Zhivago...


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Re: [Freesurfer] mri_vol2surf

[Zhivago]

Hi,

>From whatever I read, there seem to be 2 ways for overlaying activation
maps on surfaces.

1) automatic/manual registration of activation volume to orig.mgz and usage
of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be
overlaid on an inflated surface in freeview or tksurfer using the
register.dat.

2) automatic/manual registration of activation volume to orig.mgz and
overlay the activation volume on the inflated surface in tksurfer using the
register.dat

I want to know if both these are valid methods and if so, what are the pros
and cons of each.  Seems like mri_vol2surf lets us decide what part of the
volume should be projected on the surface using the projfac arguments.  But
the direct volume overlay in tksurfer doesn't provide that option.  In that
case what part of the volume is projected on to the surface?

Thanks,
Zhivago...

On Sun, Jan 15, 2017 at 10:12 PM, Zhivago  wrote:

> Thanks Bruce!  Appreciate all the help,
>
> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl  > wrote:
>
>> 1) This is up to you. Jon Polimeni had a nice paper describing the
>> trade-off between accurately representing the local neural response (which
>> is best at the white border) and statistical power (which is best nearer
>> the pial surface).
>>
>> 2) This is also up to you.Read the help in mri_vol2surf. e.g.:
>>
>> mri_vol2surf --help
>> .
>> .
>> .
>>--projfrac-avg min max del : average along normal
>>
>> 3) it is the way that we support.
>>
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 15 Jan 2017, Zhivago wrote:
>>
>> Hey Bruce,
>>>
>>> Thank you very much for the responses!  Had posted a couple of more
>>> questions, but looks like it hasn't gone across.  Will really appreciate
>>> it
>>> if you can provide some answers to these.
>>>
>>> 1) The mri_vol2surf is used to project the activations from the GM onto
>>> an
>>> inflated surface, which is usually the inflated smoothwm surface output
>>> from
>>> reconall.  Will it be more accurate to use the inflated version of the
>>> intermediate surface, like halfway between the white and pial matter?
>>> Will
>>> it make any kind of sense?
>>>
>>> 2) When mri_vol2surf projects a volume to a surface, does it average the
>>> activation values of voxels along the cortical depth or sum it?  What
>>> really
>>> happens beneath?  Any amount of insight will be helpful.
>>>
>>> 3) Is mri_vol2surf the only way to view activation maps on inflated
>>> surfaces
>>> or any surface?
>>>
>>> Cheers,
>>> Zhivago...
>>>
>>> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Zhivago
>>>
>>>   1) You can project from inside the ?h.white surface if
>>>   projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't
>>>   make much sense though as it starts to get arbitrary.
>>>
>>>   2) The default projfrac, as documented in the -help response, is
>>>   0.
>>>
>>>   3) Yes, 0-->white matter boundary. 1--> pial boundary.
>>>
>>>   4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1
>>>   vector, which is a scalar field over the surface.
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>
>>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>>
>>> Hi,
>>>
>>>
>>> I do not have a good understanding of the
>>> mri_vol2surf command.
>>>
>>> 1) Can this only project the part of the volume that
>>> lies between the white
>>> & pial matter?
>>> 2) What is the default projection parameter that it
>>> uses?
>>> 3) Does projection always start from the white
>>> matter, i.e. is 0 the white
>>> matter surface?
>>> 4) What is the nature of the mgh file that is
>>> created by:
>>> mri_vol2surf --src mri/spmT_0002.img --regheader
>>> s04  --interp nearest
>>> --hemi lh --o lh.sig.mgh
>>>
>>> Thanks,
>>> Zhivago...
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is

Re: [Freesurfer] mri_vol2surf

[Zhivago]

Thanks Bruce!  Appreciate all the help,

On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl 
wrote:

> 1) This is up to you. Jon Polimeni had a nice paper describing the
> trade-off between accurately representing the local neural response (which
> is best at the white border) and statistical power (which is best nearer
> the pial surface).
>
> 2) This is also up to you.Read the help in mri_vol2surf. e.g.:
>
> mri_vol2surf --help
> .
> .
> .
>--projfrac-avg min max del : average along normal
>
> 3) it is the way that we support.
>
>
> cheers
> Bruce
>
>
> On Sun, 15 Jan 2017, Zhivago wrote:
>
> Hey Bruce,
>>
>> Thank you very much for the responses!  Had posted a couple of more
>> questions, but looks like it hasn't gone across.  Will really appreciate
>> it
>> if you can provide some answers to these.
>>
>> 1) The mri_vol2surf is used to project the activations from the GM onto an
>> inflated surface, which is usually the inflated smoothwm surface output
>> from
>> reconall.  Will it be more accurate to use the inflated version of the
>> intermediate surface, like halfway between the white and pial matter?
>> Will
>> it make any kind of sense?
>>
>> 2) When mri_vol2surf projects a volume to a surface, does it average the
>> activation values of voxels along the cortical depth or sum it?  What
>> really
>> happens beneath?  Any amount of insight will be helpful.
>>
>> 3) Is mri_vol2surf the only way to view activation maps on inflated
>> surfaces
>> or any surface?
>>
>> Cheers,
>> Zhivago...
>>
>> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl > >
>> wrote:
>>   Hi Zhivago
>>
>>   1) You can project from inside the ?h.white surface if
>>   projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't
>>   make much sense though as it starts to get arbitrary.
>>
>>   2) The default projfrac, as documented in the -help response, is
>>   0.
>>
>>   3) Yes, 0-->white matter boundary. 1--> pial boundary.
>>
>>   4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1
>>   vector, which is a scalar field over the surface.
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Sun, 15 Jan 2017, Zhivago wrote:
>>
>> Hi,
>>
>>
>> I do not have a good understanding of the
>> mri_vol2surf command.
>>
>> 1) Can this only project the part of the volume that
>> lies between the white
>> & pial matter?
>> 2) What is the default projection parameter that it
>> uses?
>> 3) Does projection always start from the white
>> matter, i.e. is 0 the white
>> matter surface?
>> 4) What is the nature of the mgh file that is
>> created by:
>> mri_vol2surf --src mri/spmT_0002.img --regheader
>> s04  --interp nearest
>> --hemi lh --o lh.sig.mgh
>>
>> Thanks,
>> Zhivago...
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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Re: [Freesurfer] mri_vol2surf

[Bruce Fischl]

1) This is up to you. Jon Polimeni had a nice paper describing the 
trade-off between accurately representing the local neural response (which 
is best at the white border) and statistical power (which is best nearer 
the pial surface).


2) This is also up to you.Read the help in mri_vol2surf. e.g.:

mri_vol2surf --help
.
.
.
   --projfrac-avg min max del : average along normal

3) it is the way that we support.

cheers
Bruce


On Sun, 15 Jan 2017, Zhivago wrote:


Hey Bruce,

Thank you very much for the responses!  Had posted a couple of more
questions, but looks like it hasn't gone across.  Will really appreciate it
if you can provide some answers to these.

1) The mri_vol2surf is used to project the activations from the GM onto an
inflated surface, which is usually the inflated smoothwm surface output from
reconall.  Will it be more accurate to use the inflated version of the
intermediate surface, like halfway between the white and pial matter?  Will
it make any kind of sense?

2) When mri_vol2surf projects a volume to a surface, does it average the
activation values of voxels along the cortical depth or sum it?  What really
happens beneath?  Any amount of insight will be helpful.

3) Is mri_vol2surf the only way to view activation maps on inflated surfaces
or any surface?

Cheers,
Zhivago...

On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl 
wrote:
  Hi Zhivago

  1) You can project from inside the ?h.white surface if
  projfrac<0 and outside pial if projfrac>1. <<0 and >>1 won't
  make much sense though as it starts to get arbitrary.

  2) The default projfrac, as documented in the -help response, is
  0.

  3) Yes, 0-->white matter boundary. 1--> pial boundary.

  4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1
  vector, which is a scalar field over the surface.

  cheers
  Bruce



  On Sun, 15 Jan 2017, Zhivago wrote:

Hi,


I do not have a good understanding of the
mri_vol2surf command.

1) Can this only project the part of the volume that
lies between the white
& pial matter?
2) What is the default projection parameter that it
uses?
3) Does projection always start from the white
matter, i.e. is 0 the white
matter surface?
4) What is the nature of the mgh file that is
created by:
mri_vol2surf --src mri/spmT_0002.img --regheader
s04  --interp nearest
--hemi lh --o lh.sig.mgh

Thanks,
Zhivago...


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addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf

[Zhivago]

Hey Bruce,

Thank you very much for the responses!  Had posted a couple of more
questions, but looks like it hasn't gone across.  Will really appreciate it
if you can provide some answers to these.

1) The mri_vol2surf is used to project the activations from the GM onto an
inflated surface, which is usually the inflated smoothwm surface output
from reconall.  Will it be more accurate to use the inflated version of the
intermediate surface, like halfway between the white and pial matter?  Will
it make any kind of sense?

2) When mri_vol2surf projects a volume to a surface, does it average the
activation values of voxels along the cortical depth or sum it?  What
really happens beneath?  Any amount of insight will be helpful.

3) Is mri_vol2surf the only way to view activation maps on inflated
surfaces or any surface?

Cheers,
Zhivago...

On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl 
wrote:

> Hi Zhivago
>
> 1) You can project from inside the ?h.white surface if projfrac<0 and
> outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it
> starts to get arbitrary.
>
> 2) The default projfrac, as documented in the -help response, is 0.
>
> 3) Yes, 0-->white matter boundary. 1--> pial boundary.
>
> 4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector,
> which is a scalar field over the surface.
>
> cheers
> Bruce
>
>
>
>
> On Sun, 15 Jan 2017, Zhivago wrote:
>
> Hi,
>>
>>
>> I do not have a good understanding of the mri_vol2surf command.
>>
>> 1) Can this only project the part of the volume that lies between the
>> white
>> & pial matter?
>> 2) What is the default projection parameter that it uses?
>> 3) Does projection always start from the white matter, i.e. is 0 the white
>> matter surface?
>> 4) What is the nature of the mgh file that is created by:
>> mri_vol2surf --src mri/spmT_0002.img --regheader s04  --interp nearest
>> --hemi lh --o lh.sig.mgh
>>
>> Thanks,
>> Zhivago...
>>
>>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] mri_vol2surf

[Bruce Fischl]

Hi Zhivago

1) You can project from inside the ?h.white surface if projfrac<0 and 
outside pial if projfrac>1. <<0 and >>1 won't make much sense though as it 
starts to get arbitrary.


2) The default projfrac, as documented in the -help response, is 0.

3) Yes, 0-->white matter boundary. 1--> pial boundary.

4) The .mgh/.mgz file create by vol2surf is an nvertices x 1 x 1 vector, 
which is a scalar field over the surface.


cheers
Bruce



On Sun, 15 Jan 2017, Zhivago wrote:


Hi,


I do not have a good understanding of the mri_vol2surf command.

1) Can this only project the part of the volume that lies between the white
& pial matter?
2) What is the default projection parameter that it uses?
3) Does projection always start from the white matter, i.e. is 0 the white
matter surface?
4) What is the nature of the mgh file that is created by:
mri_vol2surf --src mri/spmT_0002.img --regheader s04  --interp nearest
--hemi lh --o lh.sig.mgh

Thanks,
Zhivago...

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Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

thanks Bruce

I could not find identity.nofile anywhere, when I ran mri_vol2surf I got
the following error

trisanna@kaplan:~$ mri_vol2surf --mov
/data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
/data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
srcreg = identity.nofile
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
regio_read_register(): No such file or directory
Could not open identity.nofile



Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> you can give the transformation "file" named identity.nofile and it will
> assume that the transform is the identity. You can then use mri_vol2label
> to sample the label onto the surface and visualize it with:
>
> freeview -f lh.inflated:label=lh.labels.label
>
> or some such
>
> cheers
> Bruce
>
> On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
>
> Hi there
>>
>> Just to reiterate my point above, when I open a surface created in
>> Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
>> transformations have been performed) I get the following snapshot
>> #1. Clearly, my original labels are aligned with the surface, as they
>> should
>> be since Freesurfer did not alter the space. So, how can I use mrivol2surf
>> to resample the surface such that the vertices carry the label info? What
>> output format should I use in mrivol2surf? How can I open this output in
>> Freeview?
>>
>> For instance, when I try a .dat that creates no transformation and save
>> the
>> output as .mgz and use Overlay in Freeview, I get snapshot #2. So,
>> something
>> is going wrong in my mrivol2surf command.
>>
>> My apologies for the questions
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Thu, Apr 14, 2016 at 12:08 PM, Trisanna Sprung-Much
>>  wrote:
>>   will try this, thanks.
>>
>> In the meantime
>>
>> After doing some thinking about the command, I am now confused about
>> why I need to generate a .dat in the first place. here is my thinking:
>>
>> my labels and my icbm volumes are either registered to MNI305 or
>> MNI152 template - i.e. when I painted my voxels to generate my labels,
>> the volumes were already registered to either of these templates when
>> using an in-house software.
>>
>> So, why do I want to do ANOTHER registration of mni152reg to generate
>> a .dat file that is then needed for mri_vol2surf? Why can't I simply
>> create my surfaces in Freesurfer and then overlay my labels onto those
>> surfaces if, as I have found online, Freesurfer does not change the
>> space of the input volumes? My understanding is that it calculates an
>> MNI305 transformation but does not alter the actual input space.
>> Therefore, I do not want to do any further transformations since my
>> labels and volumes are already in sync. If mri_vol2surf really needs a
>> .dat to run, shouldn't I be creating a registration matrix that does
>> absolutely nothing to ensure my labels don't change?
>>
>> Some clarification would be greatly appreciated!
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve
>>  wrote:
>>   Sorry, that is something we put in for version 6 to be
>>   able to run under
>>   newer versions of mac. Edit the file and remove the
>>   following line
>>   source $FREESURFER_HOME/sources.csh
>>
>>   On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
>>   > thanks, Doug. *Unfortunately, I got a different error
>>   this time:*
>>   >
>>   > trisanna@kaplan:~$ mni152reg --s icbm-102
>>   > /usr/local/freesurfer-5.3//sources.csh: No such file or
>>   directory.
>>   >
>>   >
>>   > What does this mean?
>>   >
>>   > After doing some thinking about the command, *I am now
>>   confused about
>>   > why I need to generate a .dat in the first place. here
>>   is my thinking:*
>>   >
>>   > my labels and my icbm volumes are either registered to
>>   MNI305 or
>>   > MNI152 template - i.e. when I painted my voxels to
>>   generate my labels,
>>   > the volumes were already registered to either of these
>>   templates when
>>   > using an in-house software.
>>   >
>>   > So, why do I want to do ANOTHER registration of
>>   mni152reg to generate
>>   > a .dat file that is then needed for mri_vol2surf? Why
>>   can't I simply
>>   > create my surfaces in Freesurfer and then overlay my
>>   labels onto those
>>   > 

Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

will try this, thanks.

In the meantime

After doing some thinking about the command, *I am now confused about why I
need to generate a .dat in the first place. here is my thinking:*

my labels and my icbm volumes are either registered to MNI305 or MNI152
template - i.e. when I painted my voxels to generate my labels, the volumes
were already registered to either of these templates when using an in-house
software.

So, why do I want to do ANOTHER registration of mni152reg to generate a
.dat file that is then needed for mri_vol2surf? Why can't I simply create
my surfaces in Freesurfer and then overlay my labels onto those surfaces
if, as I have found online,* Freesurfer does not change the space of the
input volumes?* My understanding is that it calculates an MNI305
transformation but does not alter the actual input space. Therefore, I do
not want to do any further transformations since my labels and volumes are
already in sync. If mri_vol2surf really needs a .dat to run,
*shouldn't I be creating a registration matrix that does absolutely nothing
to ensure my labels don't change?*
Some clarification would be greatly appreciated!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Apr 14, 2016 at 11:33 AM, Douglas N Greve  wrote:

> Sorry, that is something we put in for version 6 to be able to run under
> newer versions of mac. Edit the file and remove the following line
> source $FREESURFER_HOME/sources.csh
>
> On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
> > thanks, Doug. *Unfortunately, I got a different error this time:*
> >
> > trisanna@kaplan:~$ mni152reg --s icbm-102
> > /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
> >
> >
> > What does this mean?
> >
> > After doing some thinking about the command, *I am now confused about
> > why I need to generate a .dat in the first place. here is my thinking:*
> >
> > my labels and my icbm volumes are either registered to MNI305 or
> > MNI152 template - i.e. when I painted my voxels to generate my labels,
> > the volumes were already registered to either of these templates when
> > using an in-house software.
> >
> > So, why do I want to do ANOTHER registration of mni152reg to generate
> > a .dat file that is then needed for mri_vol2surf? Why can't I simply
> > create my surfaces in Freesurfer and then overlay my labels onto those
> > surfaces if, as I have found online,*Freesurfer does not change the
> > space of the input volumes?* My understanding is that it calculates an
> > MNI305 transformation but does not alter the actual input space.
> > Therefore, I do not want to do any further transformations since my
> > labels and volumes are already in sync. If mri_vol2surf really needs a
> > .dat to run, *shouldn't I be creating a registration matrix that does
> > absolutely nothing to ensure my labels don't change?
> > *
> > Some clarification would be greatly appreciated!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve
> > > wrote:
> >
> >
> > this is a known bug. Try this version instead
> >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
> >
> > On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
> > > Hi Doug
> > >
> > > So I tried running mni152reg and had the following error:
> > >
> > > mni152reg --s icbm-102_test
> > >
> > >
> > > setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
> > > cd /home/trisanna
> > > /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test
> > >
> > >
> > > fslregister --mov
> > > /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s
> > > icbm-102_test --reg
> > >
> >
>  /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
> > > --dof 12
> > > mkdir: cannot create directory
> > > ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’:
> Permission
> > > denied
> > >
> > > I spoke with our IT guy and he says that of course I cannot be
> > writing
> > > to fsl/5.0/data. I then did a web search and found that someone
> else
> > > was having this problem
> > >
> > >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
> > >
> > > How might I fix this? Let me know if I should send the log file
> that
> > > was created.
> > >
> > > best
> > >
> > > Trisanna
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve
> > > 
> >  > 

Re: [Freesurfer] mri_vol2surf misaligment

[Douglas N Greve]

I can't tell anything from that image. How do you know it is wrong? Did 
you look at the registration using tkregister? Does 
Katkov_OT_45_LH.nii.gz look ok on the surface? The problem could be in 
load_nii and/or save_nii. These are not our programs. You might try 
MRIread() and MRIwrite().

On 04/14/2016 09:54 AM, Francesca Strappini wrote:
> Hi, I think that somehow my answer  did not arrive...
> I used load_nii and save_nii to read and write out the volume. I 
> attached a picture that shows the misalignment.
>
> Thanks!
> Francesca
>
> 2016-04-08 18:31 GMT+02:00 Douglas N Greve  >:
>
> can you show a pic? What were your matlab commands to read in and
> write
> out the volume?
>
> On 04/04/2016 07:36 AM, Francesca Strappini wrote:
> > Dear Freesurfers,
> >
> > I run the preprocessing step of some functional data with
> > preproc-sess, then the Fourier analysis with matlab. Now, I'm trying
> > to plot this data on the surface:
> >
> > mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh
> > --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz
> >
> > I used as registration matrix the one produced by the preprocessing
> > step but when I try to visualize the map on the surface it looks
> like
> > completely misaligned.
> >
> > Thank you
> > Best
> > Francesca
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584 
> > E-mail: francesca.strapp...@weizmann.ac.il
> 
> >  >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_vol2surf after recon-all

[Douglas N Greve]

Sorry, that is something we put in for version 6 to be able to run under 
newer versions of mac. Edit the file and remove the following line
source $FREESURFER_HOME/sources.csh

On 04/14/2016 10:31 AM, Trisanna Sprung-Much wrote:
> thanks, Doug. *Unfortunately, I got a different error this time:*
>
> trisanna@kaplan:~$ mni152reg --s icbm-102
> /usr/local/freesurfer-5.3//sources.csh: No such file or directory.
>
>
> What does this mean?
>
> After doing some thinking about the command, *I am now confused about 
> why I need to generate a .dat in the first place. here is my thinking:*
>
> my labels and my icbm volumes are either registered to MNI305 or 
> MNI152 template - i.e. when I painted my voxels to generate my labels, 
> the volumes were already registered to either of these templates when 
> using an in-house software.
>
> So, why do I want to do ANOTHER registration of mni152reg to generate 
> a .dat file that is then needed for mri_vol2surf? Why can't I simply 
> create my surfaces in Freesurfer and then overlay my labels onto those 
> surfaces if, as I have found online,*Freesurfer does not change the 
> space of the input volumes?* My understanding is that it calculates an 
> MNI305 transformation but does not alter the actual input space. 
> Therefore, I do not want to do any further transformations since my 
> labels and volumes are already in sync. If mri_vol2surf really needs a 
> .dat to run, *shouldn't I be creating a registration matrix that does 
> absolutely nothing to ensure my labels don't change?
> *
> Some clarification would be greatly appreciated!
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve 
> > wrote:
>
>
> this is a known bug. Try this version instead
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
>
> On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So I tried running mni152reg and had the following error:
> >
> > mni152reg --s icbm-102_test
> >
> >
> > setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
> > cd /home/trisanna
> > /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test
> >
> >
> > fslregister --mov
> > /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s
> > icbm-102_test --reg
> >
> 
> /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
> > --dof 12
> > mkdir: cannot create directory
> > ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission
> > denied
> >
> > I spoke with our IT guy and he says that of course I cannot be
> writing
> > to fsl/5.0/data. I then did a web search and found that someone else
> > was having this problem
> >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
> >
> > How might I fix this? Let me know if I should send the log file that
> > was created.
> >
> > best
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > not sure, mni152reg uses
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
> >
> > You can always just run the following command directly
> >
> > fslregister --mov icbm.nii.gz --s $subject --reg
> > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
> >   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
> >
> > This will use a linear (12 dof) registration which might not be
> > particularly accurate
> >
> >
> > On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I'll get started on running all brains using
> > recon-all.
> > >
> > > The MNI has several ICBM templates now:
> > >
> > > ICBM152 linear
> > > ICBM152 nonlinear symmetric VI
> > > ICBM152 nonlinear 2009
> > >
> > > Do you know which one mni152reg is using?
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > >  
> >
> >  

Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

thanks, Doug. *Unfortunately, I got a different error this time:*

trisanna@kaplan:~$ mni152reg --s icbm-102
/usr/local/freesurfer-5.3//sources.csh: No such file or directory.


What does this mean?

After doing some thinking about the command, *I am now confused about why I
need to generate a .dat in the first place. here is my thinking:*

my labels and my icbm volumes are either registered to MNI305 or MNI152
template - i.e. when I painted my voxels to generate my labels, the volumes
were already registered to either of these templates when using an in-house
software.

So, why do I want to do ANOTHER registration of mni152reg to generate a
.dat file that is then needed for mri_vol2surf? Why can't I simply create
my surfaces in Freesurfer and then overlay my labels onto those surfaces
if, as I have found online,* Freesurfer does not change the space of the
input volumes?* My understanding is that it calculates an MNI305
transformation but does not alter the actual input space. Therefore, I do
not want to do any further transformations since my labels and volumes are
already in sync. If mri_vol2surf really needs a .dat to run,
*shouldn't I be creating a registration matrix that does absolutely nothing
to ensure my labels don't change?*
Some clarification would be greatly appreciated!

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Apr 13, 2016 at 5:06 PM, Douglas N Greve 
wrote:

>
> this is a known bug. Try this version instead
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
>
> On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
> > Hi Doug
> >
> > So I tried running mni152reg and had the following error:
> >
> > mni152reg --s icbm-102_test
> >
> >
> > setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
> > cd /home/trisanna
> > /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test
> >
> >
> > fslregister --mov
> > /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s
> > icbm-102_test --reg
> >
> /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
> > --dof 12
> > mkdir: cannot create directory
> > ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission
> > denied
> >
> > I spoke with our IT guy and he says that of course I cannot be writing
> > to fsl/5.0/data. I then did a web search and found that someone else
> > was having this problem
> >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
> >
> > How might I fix this? Let me know if I should send the log file that
> > was created.
> >
> > best
> >
> > Trisanna
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve
> > > wrote:
> >
> > not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
> >
> > You can always just run the following command directly
> >
> > fslregister --mov icbm.nii.gz --s $subject --reg
> > $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
> >   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
> >
> > This will use a linear (12 dof) registration which might not be
> > particularly accurate
> >
> >
> > On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I'll get started on running all brains using
> > recon-all.
> > >
> > > The MNI has several ICBM templates now:
> > >
> > > ICBM152 linear
> > > ICBM152 nonlinear symmetric VI
> > > ICBM152 nonlinear 2009
> > >
> > > Do you know which one mni152reg is using?
> > >
> > > Trisanna
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > >
> > >
> > > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > > > thanks, Doug. I am still extremely confused, however. *Am
> > I meant to
> > > > run recon-all first? *I was told in a previous email that I
> > > should do
> > > > this first, however, I thought that Freesurfer takes the
> > volumes and
> > > > does a linear registration to MNI305 template, which would
> > not work
> > > > for my scans that are linearly registered to ICBM152
> > nonlinear 2006
> > > > template...
> > > run recon-all first, otherwise you won't have surfaces.
> > recon-all
> > > computes the transform matrix to the mni305 but keeps all
> > the data in
> > > the native anatomical space. I think the ICBM152 is the same
> > as 

Re: [Freesurfer] mri_vol2surf after recon-all

[Douglas N Greve]

this is a known bug. Try this version instead
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> So I tried running mni152reg and had the following error:
>
> mni152reg --s icbm-102_test
>
>
> setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
> cd /home/trisanna
> /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test
>
>
> fslregister --mov 
> /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s 
> icbm-102_test --reg 
> /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat 
> --dof 12
> mkdir: cannot create directory 
> ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission 
> denied
>
> I spoke with our IT guy and he says that of course I cannot be writing 
> to fsl/5.0/data. I then did a web search and found that someone else 
> was having this problem
>
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
>
> How might I fix this? Let me know if I should send the log file that 
> was created.
>
> best
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve 
> > wrote:
>
> not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
>
> You can always just run the following command directly
>
> fslregister --mov icbm.nii.gz --s $subject --reg
> $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
>   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
>
> This will use a linear (12 dof) registration which might not be
> particularly accurate
>
>
> On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I'll get started on running all brains using
> recon-all.
> >
> > The MNI has several ICBM templates now:
> >
> > ICBM152 linear
> > ICBM152 nonlinear symmetric VI
> > ICBM152 nonlinear 2009
> >
> > Do you know which one mni152reg is using?
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> >
> >
> > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I am still extremely confused, however. *Am
> I meant to
> > > run recon-all first? *I was told in a previous email that I
> > should do
> > > this first, however, I thought that Freesurfer takes the
> volumes and
> > > does a linear registration to MNI305 template, which would
> not work
> > > for my scans that are linearly registered to ICBM152
> nonlinear 2006
> > > template...
> > run recon-all first, otherwise you won't have surfaces.
> recon-all
> > computes the transform matrix to the mni305 but keeps all
> the data in
> > the native anatomical space. I think the ICBM152 is the same
> as the
> > MNI152. Is that right? If so, you can use mni152reg to
> compute the
> > registration to 152 space. If not, then we'll have to workout
> > something
> > else.
> > >
> > > When you have a moment, could you please outline in a step
> by step
> > > manner the steps I should run to take my labels.mnc and my
> volumes
> > > such that I can generate surfaces for those 50 volumes,
> overlay the
> > > labels (for which I thought I was using mri_vol2surf) and
> then edit
> > > those labels to make them more accurate?
> > so you want to transfer the labels from labels.mnc to the
> surfaces of
> > your individual 50 subjects? Start by running recon-all on
> the 50.
> > > *The idea is that I want to generate some sulcal
> probability maps
> > > using surface-based registration, as I can already generate
> > > probability maps using volumetric registration quite easily.*
> > >
> > > many thanks
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > >  
> >
> >  
> > 

Re: [Freesurfer] mri_vol2surf after recon-all

[Trisanna Sprung-Much]

Hi Doug

So I tried running mni152reg and had the following error:

mni152reg --s icbm-102_test


setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
cd /home/trisanna
/usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test


fslregister --mov
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s
icbm-102_test --reg
/data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
--dof 12
mkdir: cannot create directory
‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission denied

I spoke with our IT guy and he says that of course I cannot be writing to
fsl/5.0/data. I then did a web search and found that someone else was
having this problem

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html

How might I fix this? Let me know if I should send the log file that was
created.

best

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve 
wrote:

> not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
>
> You can always just run the following command directly
>
> fslregister --mov icbm.nii.gz --s $subject --reg
> $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
>   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
>
> This will use a linear (12 dof) registration which might not be
> particularly accurate
>
>
> On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I'll get started on running all brains using recon-all.
> >
> > The MNI has several ICBM templates now:
> >
> > ICBM152 linear
> > ICBM152 nonlinear symmetric VI
> > ICBM152 nonlinear 2009
> >
> > Do you know which one mni152reg is using?
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > > wrote:
> >
> >
> >
> > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I am still extremely confused, however. *Am I meant
> to
> > > run recon-all first? *I was told in a previous email that I
> > should do
> > > this first, however, I thought that Freesurfer takes the volumes
> and
> > > does a linear registration to MNI305 template, which would not work
> > > for my scans that are linearly registered to ICBM152 nonlinear 2006
> > > template...
> > run recon-all first, otherwise you won't have surfaces. recon-all
> > computes the transform matrix to the mni305 but keeps all the data in
> > the native anatomical space. I think the ICBM152 is the same as the
> > MNI152. Is that right? If so, you can use mni152reg to compute the
> > registration to 152 space. If not, then we'll have to workout
> > something
> > else.
> > >
> > > When you have a moment, could you please outline in a step by step
> > > manner the steps I should run to take my labels.mnc and my volumes
> > > such that I can generate surfaces for those 50 volumes, overlay the
> > > labels (for which I thought I was using mri_vol2surf) and then edit
> > > those labels to make them more accurate?
> > so you want to transfer the labels from labels.mnc to the surfaces of
> > your individual 50 subjects? Start by running recon-all on the 50.
> > > *The idea is that I want to generate some sulcal probability maps
> > > using surface-based registration, as I can already generate
> > > probability maps using volumetric registration quite easily.*
> > >
> > > many thanks
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > > 
> >  > >> wrote:
> > >
> > > For the 152, you can run mni152reg --s subject, then specify
> > > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> > > the argument to --reg. I'll need to figure out how to generate
> a
> > > .dat/.lta for the 305.
> > >
> > >
> > >
> > > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
> > >> Any ideas?
> > >>
> > >> Trisanna
> > >>
> > >> --
> > >> Ph.D. Candidate
> > >> McGill University
> > >> Integrated Program in Neuroscience
> > >> Psychology
> > >>
> > >>
> > >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
> > >>  > 
> > >>  >

Re: [Freesurfer] mri_vol2surf after recon-all

[Douglas N Greve]

not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

You can always just run the following command directly

fslregister --mov icbm.nii.gz --s $subject --reg 
$SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
  --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta

This will use a linear (12 dof) registration which might not be 
particularly accurate


On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> thanks, Doug. I'll get started on running all brains using recon-all.
>
> The MNI has several ICBM templates now:
>
> ICBM152 linear
> ICBM152 nonlinear symmetric VI
> ICBM152 nonlinear 2009
>
> Do you know which one mni152reg is using?
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve 
> > wrote:
>
>
>
> On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I am still extremely confused, however. *Am I meant to
> > run recon-all first? *I was told in a previous email that I
> should do
> > this first, however, I thought that Freesurfer takes the volumes and
> > does a linear registration to MNI305 template, which would not work
> > for my scans that are linearly registered to ICBM152 nonlinear 2006
> > template...
> run recon-all first, otherwise you won't have surfaces. recon-all
> computes the transform matrix to the mni305 but keeps all the data in
> the native anatomical space. I think the ICBM152 is the same as the
> MNI152. Is that right? If so, you can use mni152reg to compute the
> registration to 152 space. If not, then we'll have to workout
> something
> else.
> >
> > When you have a moment, could you please outline in a step by step
> > manner the steps I should run to take my labels.mnc and my volumes
> > such that I can generate surfaces for those 50 volumes, overlay the
> > labels (for which I thought I was using mri_vol2surf) and then edit
> > those labels to make them more accurate?
> so you want to transfer the labels from labels.mnc to the surfaces of
> your individual 50 subjects? Start by running recon-all on the 50.
> > *The idea is that I want to generate some sulcal probability maps
> > using surface-based registration, as I can already generate
> > probability maps using volumetric registration quite easily.*
> >
> > many thanks
> >
> > Trisanna
> >
> >
> >
> >
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > 
>  >> wrote:
> >
> > For the 152, you can run mni152reg --s subject, then specify
> > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> > the argument to --reg. I'll need to figure out how to generate a
> > .dat/.lta for the 305.
> >
> >
> >
> > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
> >> Any ideas?
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
> >>  
> >>  >> wrote:
> >>
> >> Hi Dr. Fischl
> >>
> >> I have a mixture - some of the labels were painted in the
> >> MNI305 space (older ones) and the more recent ones are
> >> registered to the ICBM152 nonlinear symmetric VI (2006)
> template.
> >>
> >> Best
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl
> >>  
> >>  >> wrote:
> >>
> >> Hi Trisanna
> >>
> >> what space are your labels in?
> >>
> >> cheers
> >> Bruce
> >> On Tue, 5 Apr 2016, Trisanna Sprung-Much
> >> wrote:
> >>
> >> > Hi Freesurfer
> >> >
> >> > I have some labels (.mnc) that are painted