Almost there Jessica. Just a few more comments on the "art of the bug
report". It is easiest for us if you put thing in a way that we can
just cut and paste from the email. Eg, if I were submitting this report
I would write:
ssh nexlin6
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS_DIR /space/sake/3/users/inverse/subjects
cd /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
unpacksdcmdir -src /space/dicomdir -targ /space/mydata -generic -run 1
scout DICOM blah
I can cut and paste those lines directly into my shell and immediately
reproduce the problem. Do you see what I mean?
This also brings up your unpacksdcmdir. The way it is now, I can't cut
and paste it. It will be better not to have any variables. Just a
command-line with all the arguments simple and resolved.
Sorry for being such a stickler on these details, but it really is in
both of our best intersts to have efficient bug reporting.
thanks!
doug
Jessica Andrews-Hanna wrote:
Hi Doug -
Does anyone know if there is an issue with mri_convert or unpacksdcmdir?
I ran mri_convert within unpacksdcmdir.
Here is what was typed at the command prompt:
unpacksdcmdir -src `/usr/pubsw/bin/findsession $subjName | grep PATH
| awk '{print $3}'` -targ ../ -cfg "$subjName"_unpack_fsl.cfg -unpackerr
The error I get is:
mri_convert /space/archive/133/siemens/
TrioTim-35006-20070814-165946-670000/670000-3-1.dcm ..//anat/
003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii --
nspmzeropad 3 --in_type siemens_dicom
ERROR: mri_convert
child killed: segmentation violation
We've used this line plenty of times with success in the past in the
Buckner lab.
Here's some useful information using bugr:
---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914
RedHat release: CentOS release 4.4 (Final)
Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64
NMR Center info (/space/freesurfer exists):
machine: nexlin6
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts
---------------------------------------------------------------------
Thanks,
Jessica
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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