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T O P I C R E V I E W
josh.bizzell
Posted - Oct 31 2007 : 1:46:59 PM There are now some example cluster scripts on the wiki. They include sample bxh2analyze, FSL and Freesurfer scripts, and can be found here:
Posted - Nov 07 2007 : 10:14:45 AM I specified the standard image in the template.fsf file to "/usr/local/fsl/data/standard/avg152T1_brain.nii.gz" . It worked out. Thanks all for the reply!
petty
Posted - Nov 07 2007 : 09:21:10 AM theres no packages folder, or .hdr extension ... its: /usr/local/fsl/data/standard/avg152T1_brain.nii.gz
wang
Posted - Nov 07 2007 : 09:04:43 AM Sorry. There seems no such a directory: /usr/local/packages/fsl/data/standard? Thanks.
josh.bizzell
Posted - Nov 07 2007 : 09:01:54 AM I don't think you'll find it there either (it's installed somewhere different than /usr/local/packages). The best solution is to change your template .fsf file to something like this:
# Standard image
set fmri(regstandard) "FSLDIR/data/standard/avg152T1_brain.hdr"
Then in your level1 script, have sed replace FSLDIR with $FSLDIR, like this:
for i in 'template.fsf'; do
sed -e 's@FSLDIR@'$FSLDIR'@g' <$i> ${OUTDIR}/FEAT_${RUN}.fsf
done
wang
Posted - Nov 07 2007 : 08:23:34 AM Thanks Gabriel.
Dichter
Posted - Nov 06 2007 : 10:35:45 PM That's because the file "/usr/local/packages/fsl/etc/standard/avg152T1_brain.hdr"
Doesn't exist in FSL 4.0. That same image can be found in: "/usr/local/packages/fsl/data/standard/avg152T1_brain.hdr"
wang
Posted - Nov 06 2007 : 10:30:49 PM Has anyone had a problem in reading the Standard image "/usr/local/packages/fsl/etc/standard/avg152T1_brain.hdr" using FSL 4.0? I got a problem when I run the FSL first level analysis through Cluster: it couldn't find the header file for the standard image. The first level analysis was completed except registration to the Standard image though.
Here is the error message: ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/fsl/bin/flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -init /mnt/users.q.shares/wang.cEAjALp65cdvaOAjrPnS/Analysis/OddEmo_FSL/20070918_33668/rawdir/INIT.mat ** ERROR (nifti_image_read): failed to find header file for 'standard' ** ERROR: nifti_image_open(standard): bad header info Error: failed to open file standard ERROR: Could not open image standard Image Exception : #22 :: Failed to read volume standard terminate called after throwing an instance of 'RBD_COMMON::BaseException' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
By the way, as shown above, I guess Cluster used cEAjALp65cdvaOAjrPnS for identifing the experiment name ATD.02? This wasn't a problem, it found the data correctly. Thanks.
josh.bizzell
Posted - Nov 05 2007 : 2:31:44 PM First, you need to log in to the head node (einstein) using your SSH client. Then, you should just copy them to your home directory, or some folder in your home directory (the first line below just changes to your home directory):
$ cd $ cp /usr/local/sge_templates/qsub_bxh2analyze.sh .
Carpenter
Posted - Nov 05 2007 : 2:27:33 PM How do you get to that?
josh.bizzell
Posted - Nov 05 2007 : 1:58:13 PM All of the sample cluster scripts have been copied to the head node under: /usr/local/sge_templates/
