here you go. I put rh there too ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lh.DKTatlas40.gcs
On 12/18/2015 05:29 PM, Schweren, LJS (med) wrote: > > No, it doesn’t exist (lh nor rh) > > Can I get it somewhere? > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* vrijdag 18 december 2015 18:28 > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] no aseg.stats after recon-all -all? > > Does //usr/local/freesurfer5/average/lh.DKTatlas40.gcs exist? > > / > > On 12/17/15 5:53 PM, Schweren, LJS (med) wrote: > > 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ------------------------------------------------------------------------ > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
