Map volume (.nii) files to surface (.mgh) using mrivol2surf command from freesurfer

volume2surface.sh

bash_root=/Users/ilkay.isik/project_folder_temp/fc_content/MRI_data/lscp_data/derivatives

# simple version
for hemi in lh rh; do
  src_file=${bash_root}/analysis/video/odata_prmtc_inMNI/level_2.gfeat/cope3.feat/thresh_zstat1.nii.gz
  src_name=${src_file##*/} # take everything after the last /
  out_file=${bash_root}/analysis/video/odata_prmtc_inMNI/level_2.gfeat/cope3.feat/${hemi}_${src_name%.nii*}.mgh #remove .nii.gz
  
  echo ${src_file} ${out_file}
  
  mri_vol2surf --src ${src_file} \
  --out ${out_file} \
  --trgsubject fsaverage \
  --regheader fsaverage \
  --hemi ${hemi} \
  --fwhm 5
done

old_ext=nii.gz
new_ext=mgh
for sub in {01..26}; do # loop over subjects
    subj=sub-${sub}
    for map_name in cope1 cope2 cope3; do # loops over nii files
        for hemi in lh rh; do
            # create a directory to save the created mgh files
            mkdir ${bash_root}/analysis/${subj}/task/level_2.gfeat/stats/fs
           
            echo ${subj} ${map_name} ${hemi}
          
            src_file=${bash_root}/analysis/${subj}/task/level_2.gfeat/stats/${map_name}.${old_ext}
            out_file=${bash_root}/analysis/${subj}/task/level_2.gfeat/stats/fs/${hemi}.${map_name}.${new_ext}
            
            echo ${src_file} ${out_file}
            
            mri_vol2surf --src ${src_file} \
           #--trgsubject fsaverage \ # only if output space is wanted to be fsaverage
            --out ${out_file} \
            --regheader ${subj} \
            --hemi ${hemi} \
        done
    done
done