No, it doesn’t exist (lh nor rh)

 

Can I get it somewhere?

 

 

Does /usr/local/freesurfer5/average/lh.DKTatlas40.gcs exist?

Dear Freesurfer experts,

I'm trying to get BrainSeg for 5 subjects. I'm running the following commands:

for scan in ...
do
cd $SUBJECTS_DIR
recon-all -all -subjid $scan
done

It completes recon-all, but with errors. These are the errors:

[me@mycomp]$ cat recon-all.error
------------------------------
SUBJECT [mysubj]
DATE Thu Dec 17 12:57:00 PST 2015
USER me
HOST mycomp
PROCESSOR x86_64
OS Linux
Linux emotion.ucsd.edu 2.6.18-406.el5 #1 SMP Tue Jun 2 17:25:57 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /[mypathtoSUBJECTS_DIR]/[mysubj]/scripts
CMD mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 [mysubj] lh ../surf/lh.sphere.reg /usr/local/freesurfer5/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot

[me@mycomp]$ cat error.log
GCSAread(/usr/local/freesurfer5/average/lh.DKTatlas40.gcs): could not open file

As a result, I don't have any aseg.stats, nor any aparc+aseg files. I ran mri_segstats separately, but then I only get the subcortical volumes, not the totals. If I include the --brain-vol-from-seg flag, it errors again, saying:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz --brain-vol-from-seg --ctab /usr/local/freesurfer5/FreeSurferColorLUT.txt --excludeid 0 --sum /[mypathtoSUBJECTS_DIR]/scripts/[mysubj].aseg.sum
sysname  Linux
hostname mycomp
machine  x86_64
user     me
UseRobust  0
Loading /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz
Getting Brain Volume Statistics
MRISread(/[mypathtoSUBJECTS_DIR]/(null)/surf/lh.white): could not open file
No such file or directory

I'm hoping you can help me! My goal is to get just BrainSeg for these subjects, I don't need the other outcomes. So if there is a work-around I would be happy to hear. Thank you for your help!

All my best,
Lizanne

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