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 ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
