Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file
The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default
sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab
Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp
Please let me know if you guys have a suggestion,
Thank you
Yash
do you have write permission to /tmp ?
On 02/27/2018 03:25 PM, Yash Patel wrote:
Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file
The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default
sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab
Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp
Please let me know if you guys have a suggestion,
Thank you
Yash
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
do you have write permission to /tmp ?
On 02/27/2018 03:25 PM, Yash Patel wrote:
Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.
024ns.lh.15.ctab):
could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file
The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default
sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/
colortable_desikan_killiany.txt)
Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.
024ns.lh.15.ctab):
could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab
Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp
Please let me know if you guys have a suggestion,
Thank you
Yash
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 greve@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.
Thanks for the advice. I did have permission to write into /tmp; however the HPC wouldn't allow it through the mri_segstats command line. The issue was resolved by making a directory in the tmp manually, and then mri_segstats works normally.
Thanks, Yash
On Wed, Feb 28, 2018 at 1:33 PM, Yash Patel ypatel@research.baycrest.org wrote:
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
do you have write permission to /tmp ?
On 02/27/2018 03:25 PM, Yash Patel wrote:
Hello FreeSurfer experts,
I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
Whenever I try, I receive the following error (in error.log file);
CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024n
s.lh.15.ctab):
could not open for writing CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file
The output in the command prompt is below: cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default
sysname Darwin hostname ypatel-BYOD.local machine x86_64 user ypatel UseRobust 0 Constructing seg from annotation Reading annotation /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colo
rtable_desikan_killiany.txt)
Seg base 1000 CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024n
s.lh.15.ctab):
could not open for writing No such file or directory CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): could not open file No such file or directory ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab
Interestingly, I ran the SAME code a few weeks ago, and everything worked fine. Somehow something has changed. I also made sure I have permission to /tmp
Please let me know if you guys have a suggestion,
Thank you
Yash
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 greve@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.
and does that file exist in /tmp? Is there space in /tmp?
On 02/28/2018 01:33 PM, Yash Patel wrote:
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
do you have write permission to /tmp ? On 02/27/2018 03:25 PM, Yash Patel wrote: > Hello FreeSurfer experts, > > I am attempting to run "mri_segstats --annot [subjectid] lh aparc > --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" > > Whenever I try, I receive the following error (in error.log file); > > CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): > could not open for writing > CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): > could not open file > > > The output in the command prompt is below: > cmdline mri_segstats --annot brno/661A.long.024ns lh aparc --i > vol2surf/661A.v2s.0.5pf.mgh --sum stats/661A.05pf.sum --id 1001 --id > 1002 --id 1003 --id 1005 --id 1006 --id 1007 --id 1008 --id 1009 --id > 1010 --id 1011 --id 1012 --id 1013 --id 1014 --id 1015 --id 1016 --id > 1017 --id 1018 --id 1019 --id 1020 --id 1021 --id 1022 --id 1023 --id > 1024 --id 1025 --id 1026 --id 1027 --id 1028 --id 1029 --id 1030 --id > 1031 --id 1032 --id 1033 --id 1034 --id 1035 --ctab-default > > sysname Darwin > hostname ypatel-BYOD.local > machine x86_64 > user ypatel > UseRobust 0 > Constructing seg from annotation > Reading annotation > /Users/ypatel/Documents/brno/661A.long.024ns/label/lh.aparc.annot > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) > Seg base 1000 > CTABwriteFileASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): > could not open for writing > No such file or directory > CTABreadASCII(/tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab): > could not open file > No such file or directory > ERROR: reading /tmp/mri_segstats.tmp.brno/661A.long.024ns.lh.15.ctab > > > Interestingly, I ran the SAME code a few weeks ago, and everything > worked fine. Somehow something has changed. I also made sure I have > permission to /tmp > > Please let me know if you guys have a suggestion, > > Thank you > > Yash > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Yash Patel