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Dear Lilla,
Thanks for your help.
I have used the same command in the recon-all.log file (seen bellow), but I
have a doubt for the highlighted part in the command:
"mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz mri/transforms/talairach.m3z
/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gcamri/aseg.auto_noCCseg.label_intensities.txt"
which used a predefined file from freesurfer folder. Actually, I used the
mri_aparc2aseg command with some changes, seen bellow:
mri_aparc2aseg --s mysubj --annot aparc --o
$SUBJECTS_DIR/mysubj/mri/parc.mgz
so, I am wondered if it reads the '
/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I
would appreciate it of you could help on how to correct this part.
Regards,
Mahshid
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