Re: [Freesurfer] TRACULA bvec bval read from dicom

[Yendiki, Anastasia]

Hi - If there is no error message in your scripts/trac-all.log file, that means 
that it was able to read the information from the dicoms. You can double-check 
if the gradient table was read correctly by inspecting the outputs of the 
tensor fit with: freeview --dti dmri/dtifit_V1.nii.gz dmri/dtifit_FA.nii.gz. 
Display the vectors as lines and check that they follow the shape of the main 
tracts like the corpus callosum and cingulum bundle. You just need to check 
this on one of the subjects, if they were all scanned the same way.


Best,


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of VA Research 

Sent: Wednesday, December 27, 2017 8:26:48 PM
To: Freesurfer support list
Subject: [Freesurfer] TRACULA bvec bval read from dicom

Hello,

I chose comment out the set bvecfile, bvallist, bvalfile fromt the design 
script.

>From my understanding those variable above are not needed if we have a proper 
>DICOM.

All my subjects ran without error, but,

How can I confirm that my DICOM version is compatible wtih tracula,

How do I know the gradient tables are being read from the DICOM correctly?

Thanks so much,

Joseph

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[Freesurfer] TRACULA bvec bval read from dicom

[VA Research]

Hello,

I chose comment out the set bvecfile, bvallist, bvalfile fromt the design
script.

>From my understanding those variable above are not needed if we have a
proper DICOM.

All my subjects ran without error, but,

How can I confirm that my DICOM version is compatible wtih tracula,

How do I know the gradient tables are being read from the DICOM correctly?

Thanks so much,

Joseph
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[Freesurfer] Thresholding of Monte-Carlo simulation

[yoichiro takayanagi]

Dear FS experts,
 
I’m wondering whether the Monte-Carlo
simulation accountｓ for spatial or intensity thresholds (or both).
 
Thanks,
 
Yoichiro Takayanagi___
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Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

I wouldn¹t trust resting state data that have not been properly denoised.
You should only need the structural and FIX cleaned packages for what you
are doing.  The link that I put below explains how to get HCP data onto the
fsaverage4 surface.  You will need FreeSurfer and Connectome Workbench for
this.  

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Wednesday, December 27, 2017 at 5:55 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way to
get the ICA-FIX data in the right format, as per the specifications provided
by the Lui Lab. I am also not using a local machine to do the processing (I
am using my Uni's supercomputing infrastructure), so I don't know if I can
get connectome workbench installed in order to pre-process CIFTI data.
That's why I am working with standard formats (the supercomputer has
freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and that
I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana

   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser  wrote:
> You would be better off resampling the existing CIFTI data to the fsaverage4
> surface rather than redoing the projection and smoothing in the volume.
> Instructions for getting to fsaverage are available here:
> 
> https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-
> 9.HowdoImapdatabetweenFreeSurferandHCP?
> 
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Lana Ruck
> 
> Reply-To:  Freesurfer support list 
> Date:  Wednesday, December 27, 2017 at 4:41 PM
> To:  
> Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data
> 
> As a work-around to the above issue, I did the registrations directly in FSL
> using FLIRT, and then converted the resultant fsl reg.mat files to freesurfer
> reg.dat files (using tkregister2; they all look fine). Now, all I need is to
> project these rfMRI data to fsaverage4, and I thought mri_vol2surf was the
> right way to do this.
> 
> Unfortunately, I am now having the same directory issue with mri_vol2surf (new
> error log below), where it can't find /surf/lh.white for my subject. The HCP
> pre-processed data has already been through recon-all, so there are several
> *white*surf* files to choose from for each subject, but they are not in the
> directory specified by default in MRISread (subjid/surf/).
> 
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the other
> $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message boards),
> or specifying the right directory (I've tried the --surf command with both the
> fsaverage4 path, and to multiple [subject]?h.white paths, but it just appends
> them to the non-existent default path--see below). Thus, regardless of what I
> specify, I keep getting the same error related to a default search in
> subjid/surf/.
> 
> Is there a way to point MRISread to the correct surf files, without re-doing
> recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
> subjects?
> 
> Lana
> 
>> [lruck@c5 LH_all]$ mri_vol2surf --mov
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L
>> R.img --src_type analyze --reg
>> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1L
>> R_register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
>> 

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

Matt,

Thanks for the quick reply! I'll check out that Wiki document and the 2016
Nature paper first.

The reason I have the pre-processed (but not ICA-FIX'ed) rfMRI data is
because I would like to use the iterative parcellation algorithm from the
Liu Lab @Harvard (as described in Wang, D. et al. 2015: Parcellating
Cortical Functional Networks in Individuals. Nat. Neurosci;
http://nmr.mgh.harvard.edu/bid/DownLoad.html), but I am unsure if the
ICA-FIX data are appropriate for this. I know that the minimally
pre-processed rfMRI data just need to be smoothed and projected to
fsaverage4 for the MATLAB algorithm to work, but I didn't see a clear way
to get the ICA-FIX data in the right format, as per the specifications
provided by the Lui Lab. I am also not using a local machine to do the
processing (I am using my Uni's supercomputing infrastructure), so I don't
know if I can get connectome workbench installed in order to pre-process
CIFTI data. That's why I am working with standard formats (the
supercomputer has freesurfer, fsl, etc.).

Assuming I can get cnm-wb installed by admins on the supercomputer, and
that I can use it to get the ICA-FIX data appropriately formatted for
parcellation with MATLAB, do you suggest I download the extended packages,
or will the compact ones have everything I need?

Lana


Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser  wrote:

> You would be better off resampling the existing CIFTI data to the
> fsaverage4 surface rather than redoing the projection and smoothing in the
> volume.  Instructions for getting to fsaverage are available here:
>
> https://wiki.humanconnectome.org/display/PublicData/HCP+
> Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?
>
> Also I would recommend starting from the ICA+FIX cleaned data, not the
> minimally preprocessed data.  If you must smooth the data, you can do that
> with wb_command -cifti-smoothing before following the above steps.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Lana Ruck <
> lr...@umail.iu.edu>
> Reply-To: Freesurfer support list 
> Date: Wednesday, December 27, 2017 at 4:41 PM
> To: 
> Subject: Re: [Freesurfer] bbregister error -- Human Connectome Project
> Data
>
> As a work-around to the above issue, I did the registrations directly in
> FSL using FLIRT, and then converted the resultant fsl reg.mat files to
> freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
> I need is to project these rfMRI data to fsaverage4, and I thought
> mri_vol2surf was the right way to do this.
>
> Unfortunately, I am now having the same directory issue with mri_vol2surf
> (new error log below), where it can't find /surf/lh.white for my subject.
> The HCP pre-processed data has already been through recon-all, so there are
> several *white*surf* files to choose from for each subject, but they are
> not in the directory specified by default in MRISread (subjid/surf/).
>
> I thought I could fix this by specifying the right target subject
> (--trgsubject fsaverage4, which I have manually copied, along with the
> other $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
> boards), or specifying the right directory (I've tried the --surf command
> with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
> it just appends them to the non-existent default path--see below). Thus,
> regardless of what I specify, I keep getting the same error related to a
> default search in subjid/surf/.
>
> Is there a way to point MRISread to the correct surf files, without
> re-doing recon-all or moving the pre-processed surfaces to a "surf" folder
> for all 40 subjects?
>
> Lana
>
> [lruck@c5 LH_all]$ mri_vol2surf --mov /N/dc2/scratch/lruck/LH_all/
> 101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img --src_type analyze
> --reg /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR_register.dat --hemi lh --fwhm 6 --trgsubject
> fsaverage4 --surf /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white
> --out /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/
> srcvol = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR.img
> srctype = analyze
> srcreg = /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/
> rfMRI_REST1_LR/REST1LR_register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsaverage4
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
>   analyzeRead() roi_scale   0.0
> Done loading volume
> INFO: This REGISTER_DAT transform is valid only for 

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

[Matt Glasser]

You would be better off resampling the existing CIFTI data to the fsaverage4
surface rather than redoing the projection and smoothing in the volume.
Instructions for getting to fsaverage are available here:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA
Q-9.HowdoImapdatabetweenFreeSurferandHCP?

Also I would recommend starting from the ICA+FIX cleaned data, not the
minimally preprocessed data.  If you must smooth the data, you can do that
with wb_command -cifti-smoothing before following the above steps.

Peace,

Matt.

From:   on behalf of Lana Ruck

Reply-To:  Freesurfer support list 
Date:  Wednesday, December 27, 2017 at 4:41 PM
To:  
Subject:  Re: [Freesurfer] bbregister error -- Human Connectome Project Data

As a work-around to the above issue, I did the registrations directly in FSL
using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all I
need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are not
in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the other
$FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without re-doing
recon-all or moving the pre-processed surfaces to a "surf" folder for all 40
subjects?

Lana

> [lruck@c5 LH_all]$ mri_vol2surf --mov
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img --src_type analyze --reg
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat --hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
> /N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
> srcvol = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> .img
> srctype = analyze
> srcreg = 
> /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR
> _register.dat
> srcregold = 0
> srcwarp unspecified
> surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
> hemi = lh
> trgsubject = fsaverage4
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
>   analyzeRead() roi_scale   0.0
> 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 ---
>  0.96607   0.00120   0.00047  -0.78994;
>  0.01685   0.96915  -0.00899   2.16005;
> -0.00580  -0.00642   0.98726  -0.56166;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
> Reading surface 
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_a
> ll/fsaverage4/surf/lh.white): could not open file
> No such file or directory
> mri_vol2surf: could not read surface
> /N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaver
> age4/surf/lh.white
> No such file or directory


   
Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck  wrote:
> Hello, 
> 
> I am currently starting a project with the minimally pre-processed rfMRI from
> the Human Connectome Project, but I need to do some additional processing
> first. This includes smoothing at 6mm FWHM and projection onto the fsaverage4
> surface. I have smoothed the pre-processed rfMRI data using mri_convert (and
> have also converted the provided brain-extracted anatomical), but I am having
> issues registering the smoothed rfMRI volumes, and I understand that I need
> these register.dat files for mri_vol2surf.
> 
> I have tried 

[Freesurfer] About the contrast matrix in LME toolbox

[Gong, Liang]

Dear LME developer and expert,

I am using LME recently, based on longitudinal brain structural data, but I 
have two confusions in using it.

1)  I followed the tutorial at: 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
However, I don't actually understand the Contrast matrix design in this tool. 
In the example the contrast C matrix is a 3*14, is there any explain about this 
matrix design?
For my study, I want to explore 3 treatment (2 therapy methods and 1 waitlist) 
effects on the brain structural, If I want to explore the main effect of 
treatment, how could I write the Contrast matrix, and whether I can explore 
each treatment effect on the brain structural? And how can explore the 
time*treatment effect contrast matrix?

2)  For the mass-univariate analysis, the example C matrix is 3*17, and it 
will explore the group differences in the rate of change over time among the 
four groups, and if I get the four group difference maps, How can I know the 
difference between each two groups? If I need to do the another qdec file and 
do the following steps as mris_preproc and mri_surf2surf?
Thank you very much!
Best,

Gallen




X.dat
Description: X.dat


qdec.table.dat
Description: qdec.table.dat
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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] bbregister error -- Human Connectome Project Data

[Lana Ruck]

As a work-around to the above issue, I did the registrations directly in
FSL using FLIRT, and then converted the resultant fsl reg.mat files to
freesurfer reg.dat files (using tkregister2; they all look fine). Now, all
I need is to project these rfMRI data to fsaverage4, and I thought
mri_vol2surf was the right way to do this.

Unfortunately, I am now having the same directory issue with mri_vol2surf
(new error log below), where it can't find /surf/lh.white for my subject.
The HCP pre-processed data has already been through recon-all, so there are
several *white*surf* files to choose from for each subject, but they are
not in the directory specified by default in MRISread (subjid/surf/).

I thought I could fix this by specifying the right target subject
(--trgsubject fsaverage4, which I have manually copied, along with the
other $FREESURFER_HOME/subjects, to my own $SUBJECTS_DIR as per the message
boards), or specifying the right directory (I've tried the --surf command
with both the fsaverage4 path, and to multiple [subject]?h.white paths, but
it just appends them to the non-existent default path--see below). Thus,
regardless of what I specify, I keep getting the same error related to a
default search in subjid/surf/.

Is there a way to point MRISread to the correct surf files, without
re-doing recon-all or moving the pre-processed surfaces to a "surf" folder
for all 40 subjects?

Lana

[lruck@c5 LH_all]$ mri_vol2surf --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img
--src_type analyze --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
--hemi lh --fwhm 6 --trgsubject fsaverage4 --surf
/N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white --out
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/
srcvol =
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR.img
srctype = analyze
srcreg =
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
srcregold = 0
srcwarp unspecified
surf = /N/dc2/scratch/lruck/LEH_all/fsaverage4/surf/lh.white
hemi = lh
trgsubject = fsaverage4
surfreg = sphere.reg
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
  analyzeRead() roi_scale   0.0
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 ---
 0.96607   0.00120   0.00047  -0.78994;
 0.01685   0.96915  -0.00899   2.16005;
-0.00580  -0.00642   0.98726  -0.56166;
 0.0   0.0   0.0   1.0;
 original matrix ---
INFO: smoothing volume at fwhm = 6 mm (std = 2.54797)
*Reading surface
/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white*
*MRISread(/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white):
could not open file*
*No such file or directory*
*mri_vol2surf: could not read surface
/N/dc2/scratch/lruck/LH_all//101915/surf/lh./N/dc2/scratch/lruck/LH_all/fsaverage4/surf/lh.white*
*No such file or directory*




Lana Ruck, M.A.
Associate Instructor, Department of Anthropology
Graduate Scholars Fellow, Cognitive Science Program
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu


On Wed, Dec 27, 2017 at 1:43 PM, Lana Ruck  wrote:

> Hello,
>
> I am currently starting a project with the minimally pre-processed rfMRI
> from the Human Connectome Project, but I need to do some additional
> processing first. This includes smoothing at 6mm FWHM and projection onto
> the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
> mri_convert (and have also converted the provided brain-extracted
> anatomical), but I am having issues registering the smoothed rfMRI volumes,
> and I understand that I need these register.dat files for mri_vol2surf.
>
> I have tried bbregister --init-fsl; bbregister --init-spm; and manual
> registration using tkregister2. All of them give me the same error--I think
> it is a path error looking for a subject-specific brain mask (see detailed
> console errors below).
>
> After reading through others' problems with bbregister, I made sure I am
> running the updated versions of bb- and fsl-register, below:
>
> fslregister,v 1.40 2016/02/12 21:43:15 zkaufman
> bbregister,v 1.75 2016/05/10 20:02:28 greve
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
> I also made sure these files had the edits recommended to others, so I
> don't think this is an previously-addressed issue.
>
> That // in all my errors suggests to me that this is a path problem with
> my HCP data? I am new to FreeSurfer, but I would think that the
> HCP-pre-determined path organization should be compatible with FSL and
> FreeSurfer, since their pipelines use both. Is this a compatibility issue
> with FreeSurfer 6.0?
>
> Anyways, I 

[Freesurfer] Remove address

[Saturne Fox]

Is it possible to quit the freesurfer mailing list ?

Best regards,
Antoine
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[Freesurfer] bbregister error -- Human Connectome Project Data

[Lana Ruck]

Hello,

I am currently starting a project with the minimally pre-processed rfMRI
from the Human Connectome Project, but I need to do some additional
processing first. This includes smoothing at 6mm FWHM and projection onto
the fsaverage4 surface. I have smoothed the pre-processed rfMRI data using
mri_convert (and have also converted the provided brain-extracted
anatomical), but I am having issues registering the smoothed rfMRI volumes,
and I understand that I need these register.dat files for mri_vol2surf.

I have tried bbregister --init-fsl; bbregister --init-spm; and manual
registration using tkregister2. All of them give me the same error--I think
it is a path error looking for a subject-specific brain mask (see detailed
console errors below).

After reading through others' problems with bbregister, I made sure I am
running the updated versions of bb- and fsl-register, below:

fslregister,v 1.40 2016/02/12 21:43:15 zkaufman
bbregister,v 1.75 2016/05/10 20:02:28 greve
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

I also made sure these files had the edits recommended to others, so I
don't think this is an previously-addressed issue.

That // in all my errors suggests to me that this is a path problem with my
HCP data? I am new to FreeSurfer, but I would think that the
HCP-pre-determined path organization should be compatible with FSL and
FreeSurfer, since their pipelines use both. Is this a compatibility issue
with FreeSurfer 6.0?

Anyways, I would prefer to use bbregister --init-fsl, but do not know how
to point it to the right directory for a brainmask. There is no information
provided in any of the --help menus or Wiki pages regarding how to specify
brain masks for registration, and the HCP pre-processed data provides
multiple 'mask.nii.gz' files that I suppose are not being recognized by
bbregister (perhaps because they are not .mgz? I tried converting one to
mgz and also got an error from mghWrite). Either way, I have 4 rfMRI runs
per subject and over 40 subjects to process, so any advice on this error
would be greatly appreciated.

Thanks in advance!
Lana Ruck


Console errors (bolded and underlined) for bbregister --init-fsl,
bbregister --init-spm, and tkregister2:

[lruck@c5 MNINonLinear]$ bbregister --mov
./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat
tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127
Log file is
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat.log
Wed Dec 27 12:51:51 EST 2017

setenv SUBJECTS_DIR /N/dc2/scratch/lruck/LH_all/
cd /N/dc2/scratch/lruck/LH_all/101915/MNINonLinear
/N/soft/rhel6/freesurfer/6.0.0/freesurfer/bin/bbregister --mov
./Results/rfMRI_REST1_LR/REST1LR.img --bold --s 101915 --init-fsl --reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/REST1LR_register.dat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux c5.karst.uits.iu.edu 2.6.32-696.16.1.el6.x86_64 #1 SMP Sun Oct 8
09:45:56 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /N/soft/rhel6/freesurfer/6.0.0/freesurfer
mri_convert ./Results/rfMRI_REST1_LR/REST1LR.img
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
mri_convert.bin ./Results/rfMRI_REST1_LR/REST1LR.img
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./Results/rfMRI_REST1_LR/REST1LR.img...
  analyzeRead() roi_scale   0.0
TR=720.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii...
fslregister --s 101915 --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
--reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat
--niters 1 --maxangle 90 --tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister
--dof 6 --fsvol brainmask.mgz --nobetmov

Log file is
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat.fslregister.log

Wed Dec 27 12:51:52 EST 2017
--s 101915 --mov
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/template.nii
--reg
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/reg.init.dat
--niters 1 --maxangle 90 --tmp
/N/dc2/scratch/lruck/LH_all/101915/MNINonLinear/Results/rfMRI_REST1_LR/tmp.bbregister.26127/fslregister
--dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
c5.karst.uits.iu.edu
Linux 

Re: [Freesurfer] Problem flipping a label into other hemisphere

[Neuro Lists]

Hi again,
I just wanted to revisit this thread to see if I had misunderstood
something or had done something incorrectly?
The commands I used for bert were as follows:

cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere.left_right


I tried a few different combinations of mris_left_right_register but
without luck.

Thanks!


On Tue, Oct 17, 2017 at 11:55 PM, Neuro Lists 
wrote:
>
> Hi,
> The one I tested with in the last couple of messages is just the standard
bert subject after having done:
>
> cd ${SUBJECTS_DIR}/bert
> cd surf
> mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
>
> And then running:
>
> cd ../label
> mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
>
> Have I misunderstood something?
>
> Thanks again!
>
> On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve <
gr...@nmr.mgh.harvard.edu> wrote:
>>
>> Is this fsaverage or one of your own subjects?
>>
>>
>>
>> On 10/17/2017 02:18 PM, Neuro Lists wrote:
>> > Hi Doug,
>> > Thanks a lot for looking into it. Unfortunately it's still not working
>> > though.
>> >
>> > See here:
>> > https://imgur.com/a/lxXUH
>> >
>> > Thanks again!
>> >
>> > On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve
>> > > wrote:
>> >
>> > Sorry, try this
>> >
>> > mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label
>> > --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
>> >
>> >
>> > On 10/13/17 2:58 PM, Neuro Lists wrote:
>> >> Hi all,
>> >> I was just wondering if there was any further insight into what I
>> >> might be doing wrong on this.
>> >>
>> >> Thanks again!
>> >>
>> >>
>> >>
>> >> On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists
>> >> > >> > wrote:
>> >>
>> >> Hi Doug and Bruce,
>> >> I forgot to mention that I had tried that as well but without
>> >> success. As a sanity check, tried flipping a label from the
>> >> 'bert' subject and it still comes out wrong. I've uploaded a
>> >> screen shot of the result:
>> >>
>> >> https://imgur.com/a/J6Phx
>> >>
>> >> Thank you for any input you might have!
>> >>
>> >> These were the exact steps the following (I also tried
>> >> playing around with the options to --streg but without luck):
>> >>
>> >> cd ${SUBJECTS_DIR}/bert
>> >> cd surf
>> >> mris_left_right_register lh.sphere rh.sphere
>> >> lh.sphere.left_right rh.sphere.left_right
>> >> cd ../label
>> >>
>> >> mris_apply_reg --src-label lh.BA45.label --trg
>> >> lh_flip.BA45.label --streg ../surf/lh.sphere.left_right
>> >> ../surf/rh.sphere
>> >>
>> >>
>> >> $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
>> >>
>> >> cwd /home/joe/subjects/bert/label
>> >>
>> >> cmdline ../../scripts/mris_apply_reg --src-label
>> >> lh.BA45.label --trg lh_flip.BA45.label --streg
>> >> ../surf/lh.sphere.left_right ../surf/rh.sphere
>> >>
>> >> sysname  Linux
>> >>
>> >> hostname computer
>> >>
>> >> machine  x86_64
>> >>
>> >> user joe
>> >>
>> >> srcvalfile  (null)
>> >>
>> >> trgvalfile lh_flip.BA45.label
>> >>
>> >> nsurfs  2
>> >>
>> >> jac  0
>> >>
>> >> revmap  0
>> >>
>> >> 1 Loading ../surf/lh.sphere.left_right
>> >>
>> >> 2 Loading ../surf/rh.sphere
>> >>
>> >> Loading label lh.BA45.label
>> >>
>> >>4060 points in input label
>> >>
>> >> MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1
>> >>
>> >> MRISapplyReg: building hash tables (res=16).
>> >>
>> >> MRISapplyReg: Forward Loop (133299)
>> >>
>> >> MRISapplyReg: Dividing by number of hits (133299)
>> >>
>> >> MRISapplyReg: nSrcLost = 38462
>> >>
>> >>4505 points in output label
>> >>
>> >> mris_apply_reg done
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve
>> >> > >> > wrote:
>> >>
>> >> Try
>> >>
>> >> mris_apply_reg --src-label your.lh.label --trg
>> >> your.rh.label  -streg lh.sphere.left_right rh.sphere
>> >>
>> >>
>> >> On 10/11/17 5:43 PM, Neuro Lists wrote:
>> >>> Hi all,
>> >>> I've searched the lists extensively and have not been
>> >>> able to resolve my problem. I'd greatly appreciated any
>> >>> 

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Diamond, Bram Ryder]

Hi Martin,


I will have to defer to Bruce or Doug regarding the validity of analyzing 
FreeSurfer output for your subject - although I would not recommend any 
analysis on the current state of your subject's surfaces.  After glancing at 
your data, I have a few recommendations:


  1.  You seem to be using an excessive number of control points.  Control 
points are designed for diffuse intensity normalize - using too many control 
points is unnecessary and possibly counterproductive.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPointsV6.0?highlight=%28control%29%7C%28point%29
 for more information on control points.
  2.  I've noticed that your brainmask.mgz is missing a large portion of your 
subject's cerebellum.  This most likely caused some issues down the recon-all 
pipeline so you should address this issue first.  You can change the watershed 
value to adjust the brain extraction.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0 for 
information of fixing a bad skull strip.
  3.  Since the wm.mgz has done such a poor job of identifying white matter, I 
would suggest directly editing the wm.mgz.  Of course, only edit the wm.mgz 
after first attempting to use (fewer) control points on a better skull-stripped 
brainmask.mgz.  See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for 
information on editing the wm.mgz.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Loeffler, Martin 

Sent: Saturday, December 23, 2017 4:26:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst


Dear Bruce,

Dear Bram,



Thanks a lot for having a look. Unfortunately the left hemisphere is equally 
important as the right one for our question of interest. With a lot of patience 
the recon-all has finished and the result looks surprisingly ok. I have 
additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after 
setting control points to correct errors in the wm.mgz. Some errors were 
corrected, but not all. Next I would like to correct the surfaces.

My questions:

-  I know that recon-all is not designed for such a subject. But is 
there any argument against continuing the analysis now?

-  What can I do for those errors where the wm.mgz is still false, 
despite control points?

I have uploaded the respective files.



Best,

Martin





Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram 
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Hi Martin,



We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.



Best,

Bram



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Loeffler, Martin 
>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst



Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: 
> freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von
> Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 

Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+
aseg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Secondly, how I can get the change rate after construct left -right
registration.

Thanks,
Lanbo

On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter 
wrote:

> Hi Lanbo,
>
> you could look at longitudinal changes of the left-right difference in
> volume per ROI. Or do you mean on the cortical thickness map (I have never
> done that, but probably works similarly, construct left -right
> registration, compute difference, then run the LME on that).
>
> Best, Martin
>
> Am 17.12.2017 um 17:54 schrieb lanbo Wang:
>
> Hi, all experts.
> I want to compare changes rate between left and right hemisphere of
> longitudinal data, How should I do that, how to combine xhemi with two
> stage or LME?
>
> Best,
> Lanbo
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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> Freesurfer mailing list
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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.
>
>
/usr/local/freesurfer/bin/xhemireg
--s subj_02_1.long.s02_base
$Id: xhemireg,v 1.12.4.3 2012/05/02 21:28:58 greve Exp $
Wed Dec 20 17:46:00 EST 2017
Linux localhost.localdomain 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/HD4/symptom_test/subj_02_1.long.s02_base
setenv SUBJECTS_DIR /HD4/symptom_test/ 
Wed Dec 20 17:46:00 EST 2017
Wed Dec 20 17:46:00 EST 2017
mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/orig.mgz
targvol mri/orig.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1514107653

Final tkRAS-to-tkRAS Matrix is:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;


Vox2Vox Matrix is:
-1.000   0.000   0.000   255.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/T1.mgz
targvol mri/T1.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1514410525

Final tkRAS-to-tkRAS Matrix is:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;


Vox2Vox Matrix is:
-1.000   0.000   0.000   255.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol