Dear FS experts,

I am trying to extract values for cortical thickness, surface area and volumes, 
from different functional ROIs. These cortical ROIs have been defined using SPM 
tools, and are in .nii format. My scans have been processed using FS v5.3.

Although the conversion seems to go well, the “end product” does not really 
look good, some of the extracted ROI for some subjects are empty. Does anyone 
have a clue of why?

Here is what I have done:

1) transform .nii file to .mgz file

$FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz
$FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz


2) to make sure our masks from SPM will match fsaverage templates, I did

tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5
tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5

It was fine.


3) I created a .dat file containing the registration matrix from avg152T1 onto 
fsaverage

cd $SUBJECTS_DIR/fsaverage/surf
spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg 
$REG_DIR/avg152T1_to_fsaverage.dat


4) Visualisation of the registration

tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ 
$SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage.dat --surf orig

The registration was bad, so… I manually relocate the TAL template onto the 
fsaverage template and saved a new avg152T1_to_fsaverage.dat file called 
avg152T1_to_fsaverage_edited.dat. This file is used for the next steps.


5) Visualisation of the registration of our mask onto fsaverage T1

cd $SUBJECTS_DIR/fsaverage/surf
tkmedit fsaverage T1.mgz \
  -overlay $MASKS_DIR/L_ROI.mgz \
  -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white 

tkmedit fsaverage T1.mgz \
  -overlay $MASKS_DIR/R_ROI.mgz \
  -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \
  -fthresh 0.5 \
  -surface lh.white -aux-surface rh.white 

Up to this sep, everything looks good.


6) Transformation of the ROI mask to surface and thickness

mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh
mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg 
$REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh

mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l 
$MASKS_DIR/L_ROI.label
mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l 
$MASKS_DIR/R_ROI.label


7) Extraction of the ROI surface and thickness for analyses

mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f 
$OUT_DIR/results_L_ROI_SubjID SubjID lh  
mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f 
$OUT_DIR/results_R_ROI_SubjID SubjID rh

Thanks to anyone who will be able to help me with that!

Yann
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