It has to be loaded as an overlay to a surface, not a surface itself.
On 7/3/2020 10:10 AM, Eleni Nikalexi wrote:
External Email - Use Caution
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
<dgr...@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:
External Email - Use Caution
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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