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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