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 <ypa...@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 < > gr...@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 >> 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. >> > >
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