Dear Martin, Actually, I found that it doesn't like the ~/ for /home/username
When replacing the first line in the qdec.table.dat SUBJECTS_DIR=/home/username/... and also export the SUBJECTS_DIR in the terminal with the foll path, it works nicley! Thanks again! Markus 2014-09-12 22:06 GMT+02:00 Markus Gschwind <markus.gschw...@gmail.com>: > Hi Martin! > > Thanks! > Yes, indeed typing in the command > export SUBJECTS_DIR=<subjectsdir> before starting qdec solved the first > problem... there are others to follow... > > When now writing the table stats file: > > Data table loading completed successfully. > > SUBJECTS_DIR is '~/Documents/ARNAUD/' > > mkdir -p /home/user/Documents/ARNAUD/qdec/stats_tables/ > > >> ---------------------------------------------------------- > > asegstats2table --common-segs --meas volume --tablefile >> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10 >> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 > > SUBJECTS_DIR : ~/Documents/ARNAUD/ > > Parsing the .stats files >> ERROR: The stats file ~/Documents/ARNAUD/s01/stats/aseg.stats is not >> found or is too small to be a valid statsfile >> Use --skip flag to automatically skip bad stats files >> ERROR: In >> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >> line 230 >> vtkKWQdecApp (0x28594510): >> Script: >> vtkTemp2 GenerateStatsDataTables >> Returned Error on line 1: >> Uncaught exception: command failed: asegstats2table --common-segs --meas >> volume --tablefile >> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10 >> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 >> Stack trace: >> Uncaught exception: command failed: asegstats2table --common-segs --meas >> volume --tablefile >> /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10 >> s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 >> while executing >> "vtkTemp2 GenerateStatsDataTables" > > > The file ~/Documents/ARNAUD/s01/stats/aseg.stats is very well there and > seems very normal, with plenty of numbers in it. > > The /home/user/Documents/ARNAUD/qdec/stats_tables/ folders are created, > but empty. > > Any further ideas? > Thanks ! > > Markus > > 2014-09-12 21:47 GMT+02:00 Martin Reuter <mreu...@nmr.mgh.harvard.edu>: > >> Hi Markus, >> >> maybe for some weird reason it uses the subjects_dir from the environment >> variable instead of the qdec file (that would probably be a bug). If that's >> the case, try setting the subject dir on the command line before starting >> qdec: >> setenv SUBJECTS_DIR ~/Documents/ARNAUD/ >> (or the full path). If you use a bash shell, use the equivalent export >> command for that. >> >> Best, Martin >> >> >> On 09/12/2014 03:30 PM, Markus Gschwind wrote: >> >> Dear all, >> >> I am trying to make work Qdec on my system ubuntu 12.04. >> >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> After I have loaded my qdec.table.dat and renamed the analysis folder , >> when I then try to create the "stats tables", I get an error and it blocks >> at 20% of the waiting bar. >> >> >> Data table loading completed successfully. >>> >>> SUBJECTS_DIR is '~/Documents/ARNAUD/' >>> >>> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ >>> >>> mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': >>>> Permission denied >>> >>> ERROR: In >>>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >>>> line 230 >>> >>> vtkKWQdecApp (0x289a94e0): >>> >>> Script: >>> >>> vtkTemp2 GenerateStatsDataTables >>> >>> Returned Error on line 1: >>> >>> Uncaught exception: command failed: mkdir -p >>>> /usr/local/freesurfer/subjects/qdec/stats_tables/ >>> >>> >>>> Stack trace: >>> >>> Uncaught exception: command failed: mkdir -p >>>> /usr/local/freesurfer/subjects/qdec/stats_tables/ >>> >>> >>>> while executing >>> >>> "vtkTemp2 GenerateStatsDataTables" >>> >>> >>> It seems that it tries to write into the default SUBJECT_DIR, thing >> that I do not understand as I put the actual SUBJECT_DIR in the top line of >> qdec.table.dat (and it is correctly recognized in the qdec window >> SUBJECTS_DIR). >> >> How could I come around that problem? >> >> Thanks in advance! >> Markus >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Dr. Martin Reuter >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreu...@nmr.mgh.harvard.edu >> reu...@mit.edu >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> 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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