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.
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No, it doesn't exist (lh nor rh)
Can I get it somewhere?
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.edumailto: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.
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Schweren, LJS (med)