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 <mreuter@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

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-- 
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
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Phone: +1-617-724-5652
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