Hi,
I ran into 2 problems related to tracula.
1. trac-all -bedp command exits with following message.
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri subjectdir is /usr/local/freesurfer/subjects/C001/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x53: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected
This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following:
/usr/local/fsl/bin/bedpostx_single_slice.sh /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0
then I got:
** ERROR (nifti_image_read): failed to find header file for '/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000' ** ERROR: nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000): bad header info ERROR: failed to open file /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 ERROR: Could not open image /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 Image Exception : #22 :: Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000
An exception has been thrown Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000Trace: read_volume4DROI.
Done
Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well.
My other question is: trac-all -path exists with error (in case of a single subject):
Loading DWIs from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/dwi.nii.gz Loading mask from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri.bedpostX Loading segmentation map from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/mni/aparc+aseg.nii.gz Loading b-values from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvals Loading gradients from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux
trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011
thanks for help. Judit