Hello,

I am trying to get average ROI timecourses for functional connectivity analysis where the ROIs are based on the volumetric FreeSurfer parcellation aparc.2009s+asec.

To achieve that, I tried the following commands for each subject and ROI:

@FS_roi_label -name ${ROI} -rankmap ${FSdirectory}/${subject}/SUMA/aparc.a2009s+aseg_rank.rankmap.1D > label_info.1D
labelnumber=$(1deval -ok_1D_text -a label_info.1D[0]{1} -expr 'a')
rm label_info.1D

3dmaskave -mask ${subject}_aparc.a2009s+aseg_rank_Alnd_2epi_LowRes+orig. -mrange ${labelnumber} ${labelnumber} epi_RSbas_${subject}_ppn+orig. > ${ROI}_epi_RSbas.1D


However, the output of the previous @FS_roi_label command is just "Rank Label Name" for some ROIs. For instance,

>> @FS_roi_label -name ctx_lh_G_front_middle -rankmap ../freesurfer/01C/SUMA/aparc.a2009s+aseg_rank.rankmap.1D
Rank Label Name

In addition, for some ROIs I get two possible matching names from FreeSurfer's FreeSurferColorLUT.txt, but I only want the exact matching name. How can I obtain only one value?

>> @FS_roi_label -name Left-Caudate
#11 Left-Caudate
#101 Left-caudate-intensity-abnormality
#136 Left-Caudate-Putamen

>> @FS_roi_label -name left-caudate -rankmap ../freesurfer/01C/SUMA/aparc.a2009s+aseg_rank.rankmap.1D
Rank Label Name
7 11 Left-Caudate
# 101 Left-caudate-intensity-abnormality


If necessary, please let me know how I can upload the list of ROI names I am using and the corresponding aparc.a2009s+aseg_ran.rankmap.1D file


Thanks in advance for your help,

Cesar