[Freesurfer] Longitudinal Pipeline

[AKUDJEDU, THEOPHILUS]

Hi All,

Is it standard practice to conduct  test when corrections are made in 
freesurfer for subcortical structure volumes?

Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?


Thanks


Theo


From: AKUDJEDU, THEOPHILUS
Sent: Tuesday, June 13, 2017 3:19:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal Pipeline


Hi All,


Is it standard practice to conduct reliability when corrections are made in 
freesurfer for subcortical structure volumes?


Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?



Thanks



Theo





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Re: [Freesurfer] Medial Surface Problem

[Bronwyn Overs]

Hi Bruce, 

That's fine, thanks very much. 



Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1883 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Bruce Fischl"  
To: "Freesurfer support list"  
Sent: Wednesday, 14 June, 2017 00:02:04 
Subject: Re: [Freesurfer] Medial Surface Problem 

thanks Bronwyn 

I got them. It will take a bit for us to get to as this is in the long 
stream and we have a new postdoc who will be taking it over. 

cheers 
Bruce 
On Tue, 13 Jun 
2017, Bronwyn Overs wrote: 

> Hi Bruce, 
> Sure, files have been dropped again. 
> 
> Kind regards, 
> 
> Bronwyn Overs 
> Research Assistant 
> 
> Neuroscience Research Australia 
> 
> Neuroscience Research Australia 
> Margarete Ainsworth Building 
> Barker Street Randwick Sydney NSW 2031 Australia 
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 
> 
> neura.edu.au 
> 
> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the 
> NeuRA Magazine 
> 
> 
> On 13 Jun 2017, at 11:44 am, Bruce Fischl 
>  wrote: 
> 
> Hi Bronwyn 
> Can you filedrop it again? I don't think I have it 
> Thanks 
> Bruce 
> 
> On May 15, 2017, at 8:27 PM, Bronwyn Overs  
> wrote: 
> 
> Hi Bruce, 
> Thank you for offering to take a look at this medial surface 
> problem. 
> 
> I have uploaded all of the relevant files to through the 
> Martinos Centre FileDrop v2.0 to your email address 
> (fis...@nmr.mgh.harvard.edu). Please let me know if you require 
> any additional information. 
> 
> Kind regards, 
> 
> Bronwyn Overs 
> Research Assistant 
> 
> Neuroscience Research Australia 
> 
> Neuroscience Research Australia 
> Margarete Ainsworth Building 
> Barker Street Randwick Sydney NSW 2031 Australia 
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 
> 
> neura.edu.au 
> 
> Follow @neuraustralia on twitter Follow NeuRA on facebook 
> Subscribe to the NeuRA Magazine 
> 
> 
> On 5 May 2017, at 8:25 am, Bruce Fischl 
>  wrote: 
> 
> if someone can upload a dataset as well as the exact 
> coordinates of the problem I'll take a look 
> 
> cheers 
> Bruce 
> 
> On Fri, 5 May 2017, Yann Quidé wrote: 
> 
> Hi all, 
> We also have the same issue, any 
> idea/suggestion? 
> Thanks. 
> Yann 
> 
> On 27 Apr 2017, at 9:43 am, Bronwyn Overs 
>  
> wrote: 
> Hi Mailing List, 
> Still trying to solve the below medial surface 
> problem. Does anyone 
> have any ideas? 
> Kind regards, 
> Bronwyn Overs 
> Research Assistant 
> Neuroscience Research Australia 
> Neuroscience Research Australia 
> Margarete Ainsworth Building 
> Barker Street Randwick Sydney NSW 2031 
> Australia 
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 
> 1265 
> neura.edu.au 
> Follow @neuraustralia on twitter Follow NeuRA 
> on facebook Subscribe to 
> the NeuRA Magazine 
> 
> On 28 Mar 2017, at 10:51 pm, Yann Quidé 
>  wrote: 
> Dear all, 
> I have an equivalent issue with my data. Any 
> idea on how to fix 
> this? 
> Thanks. 
> Yann 
> 
> Begin forwarded message: 
> From: Bronwyn Overs  
> Subject: Re: [Freesurfer] Medial Surface 
> Problem 
> Date: 20 March 2017 10:28:37 am AEDT 
> To: Freesurfer support list 
>  
> Reply-To: Freesurfer support list 
>  
> Hello again mailing list, 
> Can anyone address the possible cause of the 
> medial 
> surface problem shown below (overestimating of 
> rh medial 
> surface, shows up in the long image and not 
> the tp or base 
> images). Forgot to mention that I am using 
> freesurfer v5.3 
> with an updated mris_make_surfaces binary 
> (sourced from 
> the developmentversionat 
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binarie 
> s/cento 
> s6_x86_64/ ). 
> Here is the image again: 
>  
> Kind regards, 
> Bronwyn Overs 
> Research Assistant 
> Neuroscience Research Australia 
> Neuroscience Research Australia 
> Margarete Ainsworth Building 
> Barker Street Randwick Sydney NSW 2031 
> Australia 
> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 
> 1265 
> neura.edu.au 
> Follow @neuraustralia on twitter Follow NeuRA 
> on facebook 
> Subscribe to the NeuRA Magazine 
> 
> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs 
>  wrote: 
> Hi mailing list, 
> I am currently processing a longitudinal image 
> and 
> have come across a problem at the medial 
> surface in 
> the long image (step 3). As you can see in the 
> attached image, the rh medial surface has been 
> significantly overestimated and extends into 
> the lh 
> 

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

[Elijah Mak]

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 


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[Freesurfer] Surface area of a define volume projection on cortical surface

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

Given the well known size of a voxel I would like to know the equivalent
surface area once projected on the white fsaverage cortical surface.

Could anyone give me a proper way of computing this ?

Best regards,
Matthieu
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[Freesurfer] Applying an affine transformation to a surface

[Daniel Gallichan]

Hello

In a very similar situation to a post I found in the Freesurfer archive, I have 
low-resolution (3T) and high-resolution scans (7T) of the same subject - and 
would like to put the surfaces from the low-resolution scan into the space of 
the hi-res data. The instructions from the previous thread say to check example 
4 when running ‘mri_surf2surf --help’ - which I tried, but I cannot get the 
result to overlap in freeview.

I have a registration file which looks very good from running bbregister on the 
high-res data into the low-res space - but I cannot perform the registration 
the other way around as I’m still having trouble getting the hi-res data to 
process properly through recon-all (it’s acquired at 350um, and I’m currently 
running it downsampled to 500um, but that’s still a work-in-progress…).

So this is the command-line that I tried to apply the transformation from the 
registration to a surface:

mri_surf2surf --reg-inv hires_to_lowres.dat 
${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --hemi lh --sval-xyz white --tval-xyz 
${SUBJECTS_DIR}/subj_hires/mri/T1.mgz --tval lh.white.hires --s subj_lowres

If I then try to view the result:

freeview -v ${SUBJECTS_DIR}/subj_hires/mri/T1.mgz -f 
${SUBJECTS_DIR}/subj_lowres/surf/lh.white.hires

it is clear that the two are far from being aligned…

I’m afraid I may be misunderstanding how to control the coordinate systems in 
the mri_surf2surf command - especially as the source and targets are different 
’subjects’ (the same actual subject, though…). I can’t used the ‘--trgsubject’ 
option because recon-all has not completed properly on the hires data, and 
there is no sphere.reg file (although I have to confess, I haven’t understood 
why it would need it if I am specifying my own registration file…) . Any 
suggestions very gratefully received.

Thanks

Daniel












Dr Daniel Gallichan
Lecturer

CUBRIC
School of Engineering
Cardiff University
Maindy Road
Cardiff
CF24 4HQ
Wales, United Kingdom

Tel: +44 (0) 29 208 70045
Email: 
gallich...@cardiff.ac.uk


Dr Daniel Gallichan
Ddarlithydd

CUBRIC
Ysgol Beirianneg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
Cymru, y Deyrnas Unedig

Ffôn: +44 (0) 29 208 70045
E-bost: gallich...@caerdydd.ac.uk


  Personal website:  
http://www.cardiff.ac.uk/people/view/507850-gallichan-daniel
  CUBRIC - Cardiff University Brain Research Imaging Centre - 
http://sites.cardiff.ac.uk/cubric/

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Re: [Freesurfer] Libnetcdf.so.6 error during mris_make_surfaces

[Z K]

Hello Lisa,

Can you provide me with the contents of your 
FREESURFER_HOME/build-stamp.txt file

On 06/12/2017 05:44 PM, Lisa Kramarenko wrote:
> Hi,
> 
> I am getting the following error when my HCP pipelines come to the 
> mris_make surfaces step:
> 
> mris_make_surfaces: error while loading shared libraries: 
> libnetcdf.so.6: cannot open shared object file: No such file or directory
> 
> I saw this response: 
> https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02418.html 
> but the files are not available anymore and I cannot find where to 
> download it. I have Ubuntu 14.04 (64-bit). Do you have any idea about 
> what causes this problem and how to solve it?
> 
> Thanks a lot!
> Lisa
> 
> 
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Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Hi Doug,

After resampling the aparc annotation into the functional native space, the LUT 
values no longer correspond to the correct regions. A screenshot is attached 
here: http://i.imgur.com/HNIgrKI.png

The values for the labels range from 1 - 35 only.

The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp 
${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh 
--subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii

The goal is to apply the annotation and extract the regional fMRI data (4D) 
using this 3D volume parcellation. Could we achieve that by using these steps?

Thanks.

Best Wishes,
Elijah



On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll have to 
do something like

mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
Elijah


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[Freesurfer] Longitudinal Pipeline

[AKUDJEDU, THEOPHILUS]

Hi All,


Is it standard practice to conduct reliability when corrections are made in 
freesurfer for subcortical structure volumes?


Also, are you able to analyse data acquired (1.5T - time point one) with 
time-point two (3T) in the longitudinal pipeline?



Thanks



Theo





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Re: [Freesurfer] Medial Surface Problem

[Bruce Fischl]

thanks Bronwyn

I got them. It will take a bit for us to get to as this is in the long 
stream and we have a new postdoc who will be taking it over.


cheers
Bruce
On Tue, 13 Jun 
2017, Bronwyn Overs wrote:



Hi Bruce,
Sure, files have been dropped again.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the
NeuRA Magazine


  On 13 Jun 2017, at 11:44 am, Bruce Fischl
   wrote:

Hi Bronwyn 
Can you filedrop it again? I don't think I have it
Thanks
Bruce

On May 15, 2017, at 8:27 PM, Bronwyn Overs 
wrote:

  Hi Bruce,
Thank you for offering to take a look at this medial surface
problem.

I have uploaded all of the relevant files to through the
Martinos Centre FileDrop v2.0 to your email address
(fis...@nmr.mgh.harvard.edu). Please let me know if you require
any additional information.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265

neura.edu.au

Follow @neuraustralia on twitter Follow NeuRA on facebook
Subscribe to the NeuRA Magazine


  On 5 May 2017, at 8:25 am, Bruce Fischl
   wrote:

if someone can upload a dataset as well as the exact
coordinates of the problem I'll take a look

cheers
Bruce

On Fri, 5 May 2017, Yann Quidé wrote:

  Hi all,
  We also have the same issue, any
  idea/suggestion?
  Thanks.
  Yann

   On 27 Apr 2017, at 9:43 am, Bronwyn Overs
  
   wrote:
  Hi Mailing List,
  Still trying to solve the below medial surface
  problem. Does anyone
  have any ideas?
  Kind regards,
  Bronwyn Overs
  Research Assistant
  Neuroscience Research Australia
  Neuroscience Research Australia
  Margarete Ainsworth Building
  Barker Street Randwick Sydney NSW 2031
  Australia
  M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
  1265
  neura.edu.au
  Follow @neuraustralia on twitter Follow NeuRA
  on facebook Subscribe to
  the NeuRA Magazine

   On 28 Mar 2017, at 10:51 pm, Yann Quidé
    wrote:
  Dear all,
  I have an equivalent issue with my data. Any
  idea on how to fix
  this?
  Thanks.
  Yann

   Begin forwarded message:
  From: Bronwyn Overs 
  Subject: Re: [Freesurfer] Medial Surface
  Problem
  Date: 20 March 2017 10:28:37 am AEDT
  To: Freesurfer support list
  
  Reply-To: Freesurfer support list
  
  Hello again mailing list,
  Can anyone address the possible cause of the
  medial
  surface problem shown below (overestimating of
  rh medial
  surface, shows up in the long image and not
  the tp or base
  images). Forgot to mention that I am using
  freesurfer v5.3
  with an updated mris_make_surfaces binary
  (sourced from
  the developmentversionat 
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binarie
  s/cento
  s6_x86_64/ ).
  Here is the image again:
  
  Kind regards,
  Bronwyn Overs
  Research Assistant
  Neuroscience Research Australia
  Neuroscience Research Australia
  Margarete Ainsworth Building
  Barker Street Randwick Sydney NSW 2031
  Australia
  M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
  1265
  neura.edu.au
  Follow @neuraustralia on twitter Follow NeuRA
  on facebook
  Subscribe to the NeuRA Magazine

   On 6 Mar 2017, at 1:17 pm, Bronwyn Overs
    wrote:
  Hi mailing list,
  I am currently processing a longitudinal image
  and
  have come across a problem at the medial
  surface in
  the long image (step 3). As you can see in the
  attached image, the rh medial surface has been
  significantly overestimated and extends into
  the lh
  surface. This error showed up only in only 1
  of the
  2 long images for this subject, and both the
  time-point images and the base are perfectly
  fine.
  Do you know why this is happening? 
  
  Kind regards,
  Bronwyn Overs
  Research Assistant
  Neuroscience Research Australia
  Neuroscience Research Australia
  Margarete Ainsworth Building
  Barker Street Randwick Sydney NSW 2031
  Australia
  M 0411 308 769 T +61 2 9399 1883 F +61 2 9399
  1265
  neura.edu.au
  Follow 

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Great! Many thanks, Doug.

Best Wishes,
Elijah 


On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll have to 
do something like

mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
Elijah


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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] Merging outputs of mri_label2vol across hemi

[Douglas Greve]

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll 
have to do something like


mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:

Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space 
using mri_label2vol. It works fine and the script produced the 
segmentation for each hemisphere. Is there a way to merge both the 
left and right volumes together? Thanks for your help.


Best Wishes,
Elijah


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] difference in T1 and T2 resolution

[Douglas Greve]

can you send the log file?


On 6/11/17 10:08 PM, John Anderson wrote:

In the log file the error was:
ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
Debug info: size(1) = 1, 1, 1   size(0) = 0.7, 0.7, 0.8
MultiRegistration::loadMovables: voxel size is different 
/recons/subj1/mri/orig/002.mgz.

Jon
*Sent:* Sunday, June 11, 2017 at 2:12 PM
*From:* "Matt Glasser" 
*To:* "Freesurfer support list" 
*Subject:* Re: [Freesurfer] difference in T1 and T2 resolution
What was the error message?
Peace,
Matt.
From: > on behalf of John 
Anderson >
Reply-To: Freesurfer support list >

Date: Sunday, June 11, 2017 at 9:06 AM
To: >

Subject: [Freesurfer] difference in T1 and T2 resolution
Dear Freesurfer experts,
I have T1 and T2 images were unfortunately acquired with different 
resolution (i.e the voxel sizes is not the same)

T1 is 280X280X208
T2 is 270X270X200

I tried to run "recon-all"  but it failed to process the data. The 
command that I used is :
pbsubmit -c " recon-all -subjid subj1 -T2 PATH_TO_/T2.nii.gz -qcache 
-T2pial -all"
How can I analyze these images? Is it a correct procedure to conform 
the voxels using "mri_convert". Is this procedure correct? does it 
hurt the anatomy of the images?

I highly appreciate your help
John
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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.