Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either.
I think the problem is with bash vs. sh in ubuntu (possible all debian systems). ie. /bin/sh is not the same as /bin/bash so not all bash commands will work.
I did this: sudo mv /bin/sh /bin/sh.bak sudo ln -s /bin/bash /bin/sh
and then it worked. I'm hoping this doesn't have repercussion for my other programs though.
thanks, mishkin
On Tue, Oct 7, 2008 at 11:20 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
yes, this sounds like a tough one. the VerifySubjects routine that produces that error message just runs the 'ls' command on that subject directory name, so that is why i asked. if you run the 'ls' command on '/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester', does it return a correct response? ie a non-zero status?
what does 'which ls' say? possibly it is aliased to something that is causing a problem.
does qdec work despite the error? the code is setup to just print the error, but continue anyway. if the subject doesnt exist, it will fail downstream (during mri_glmfit).
i'll try to think of other things.
nick
On Tue, 2008-10-07 at 21:26 -0400, Mishkin Derakhshan wrote:
Hi Nick, Yes I've checked most of the obvious things I could think of. The directories all exist, permissions on all files are 775, i will try 777 but don't suspect that will make a difference. My env variables seem to be set properly as well.
opus[/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester]$ . /lab1/FreeSurfer/4.0.5/quarantine/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /lab1/FreeSurfer/4.0.5/quarantine FSFAST_HOME /lab1/FreeSurfer/4.0.5/quarantine/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /lab1/FreeSurfer/4.0.5/ms-mni/testing/ MNI_DIR /lab1/FreeSurfer/4.0.5/quarantine/mni
I get the same error when trying to load the tutorial qdec.table.dat as well.
My analysis is stuck at this point so any help is greatly appreciated.
thanks, mishkin
On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Mishkin,
Does this directory exist?
/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester
The error message you are seeing is checking for the existence of that directory.
Nick
On Tue, 2008-10-07 at 14:30 -0400, Mishkin Derakhshan wrote:
Hi, When I try to load a qdec.table.dat I always get the same error:
sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR
I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tried tcsh and the bash shell. Here is a bit more information and my qdec.table.dat is attached. Any ideas on how to get qdec up and running would be very useful. thanks, mishkin
FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Debian version: lenny/sid Kernel info: Linux 2.6.24-18-generic x86_64
opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl
Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl
Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat... Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 2 Reading discrete factor levels from config file /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/gender.levels...'Male','Female', done.
Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat loaded. SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in SUBJECTS_DIR Error loading the data table. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Check out this article:
https://wiki.ubuntu.com/DashAsBinSh
/bin/sh is still just a symlink to /bin/bash on Debian.
mjp
On Oct 8, 2008, at 2:43 PM, Mishkin Derakhshan wrote:
Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either.
I think the problem is with bash vs. sh in ubuntu (possible all debian systems). ie. /bin/sh is not the same as /bin/bash so not all bash commands will work.
I did this: sudo mv /bin/sh /bin/sh.bak sudo ln -s /bin/bash /bin/sh
and then it worked. I'm hoping this doesn't have repercussion for my other programs though.
thanks, mishkin
On Tue, Oct 7, 2008 at 11:20 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
yes, this sounds like a tough one. the VerifySubjects routine that produces that error message just runs the 'ls' command on that subject directory name, so that is why i asked. if you run the 'ls' command on '/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester', does it return a correct response? ie a non-zero status?
what does 'which ls' say? possibly it is aliased to something that is causing a problem.
does qdec work despite the error? the code is setup to just print the error, but continue anyway. if the subject doesnt exist, it will fail downstream (during mri_glmfit).
i'll try to think of other things.
nick
On Tue, 2008-10-07 at 21:26 -0400, Mishkin Derakhshan wrote:
Hi Nick, Yes I've checked most of the obvious things I could think of. The directories all exist, permissions on all files are 775, i will try 777 but don't suspect that will make a difference. My env variables seem to be set properly as well.
opus[/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester]$ . /lab1/FreeSurfer/4.0.5/quarantine/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /lab1/FreeSurfer/4.0.5/quarantine FSFAST_HOME /lab1/FreeSurfer/4.0.5/quarantine/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /lab1/FreeSurfer/4.0.5/ms-mni/testing/ MNI_DIR /lab1/FreeSurfer/4.0.5/quarantine/mni
I get the same error when trying to load the tutorial qdec.table.dat as well.
My analysis is stuck at this point so any help is greatly appreciated.
thanks, mishkin
On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Mishkin,
Does this directory exist?
/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester
The error message you are seeing is checking for the existence of that directory.
Nick
On Tue, 2008-10-07 at 14:30 -0400, Mishkin Derakhshan wrote:
Hi, When I try to load a qdec.table.dat I always get the same error:
sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR
I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tried tcsh and the bash shell. Here is a bit more information and my qdec.table.dat is attached. Any ideas on how to get qdec up and running would be very useful. thanks, mishkin
FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Debian version: lenny/sid Kernel info: Linux 2.6.24-18-generic x86_64
opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl
Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl
Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ qdec.table.dat... Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 2 Reading discrete factor levels from config file /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ gender.levels...'Male','Female', done.
Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/ qdec.table.dat loaded. SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in SUBJECTS_DIR Error loading the data table. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Mark J. Pearrow -
Mishkin Derakhshan