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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