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
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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing listFreesurfer@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: mreuter@nmr.mgh.harvard.edu reuter@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.
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.gschwind@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 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
Freesurfer mailing listFreesurfer@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: mreuter@nmr.mgh.harvard.edu reuter@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.
freesurfer@nmr.mgh.harvard.edu
-
Markus Gschwind -
Martin Reuter