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Dear Bruce and Douglas,
Thank you very much for the prompt, indeed it worked. 
Since the ROIs were originally obtained in 2mm voxel size, I used the vol2surf command as you suggested, in order map the ROI all the way onto the fsaverage surface:

$ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG_tmpfs.mgh --projdist-max 0 1 0.1 --noreshape --trgsubject fsaverage

I checked the result using: 

$ freeview -f ../data/scans/subject/fsaverage/surf/lh.inflated:overlay=Left_AngG_tmpfs.mgh

and the overlay is correct.
Then, I tried to transform the Left_AngG_tmpfs.mgh to a label using the fsaverage as a reference. The command I used was: 
 
$ mri_vol2label --i Left_AngG_tmpfs.mgh --id  1 --l LeftAngG_tmp.label  --surf fsaverage lh white

but permission was denied. 
If I try to use one of my subjects as a reference I get: ERROR: dim mismatch between surface (117900) and input (163842).
What would you suggest?

Thank you in advance,
Best wishes,
Eleni

On Friday, July 3, 2020, 06:35:05 PM GMT+3, Fischl, Bruce <bfischl@mgh.harvard.edu> wrote:


Hi Eleni

 

What is your freeview command line? Note that in this case the output of mri_vol2surf is *not* a surface, but rather  a scalar field over the surface (that is, a file with one or more values per vertex location). To visualize it you need to load a surface, then load your overlay on top of it. Look at the freeview help on overlays, but it should be something like:

 

Freeview -f lh.inflated:overlay=LeftAngG_tmp.mgh

 

Cheers

Bruce

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Eleni Nikalexi
Sent: Friday, July 3, 2020 10:11 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Label on fsaverage failure

 

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Dear Douglas,

thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm).

Then I run the following command, as you suggested:

$ mri_vol2surf --mov ROI_set1/LeftAngG.img  --regheader MNI_1mm --interp nearest --hemi lh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape

 

But then, in freeview I get the following result: 

 

Inline image

I also get an error when I try to load it as a surface:

"LeftAngG_tmp.mgh' has 0 vertices!

Probably trying to use a scalar data file as a surface!"

 

What could be the mistake?

 

Best regards,

Eleni

 

 

 

On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

 

 

Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface

On 7/1/2020 10:03 AM, Eleni Nikalexi wrote:

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Dear Freesurfer developers,

 

We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm.  

We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed:

 

  1. $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat
  2. $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat
  3. $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape
  4. $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz

The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview.

 

Could you please suggest something that we could do to fix this?

 

Thank  you so much in advance!

 

Best regards,

Eleni

 



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