Dear experts,

To complete my error, I've got moreover another error in "dmri.bedpostX/logs" for each slice :

** ERROR (nifti_image_read): failed to find header file for '/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000'

** ERROR: nifti_image_open(/home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000): bad header info

Error: failed to open file /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000

ERROR: Could not open image /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000

Image Exception : #22 :: Failed to read volume /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000

An exception has been thrown

Failed to read volume /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri/data_slice_0000Trace: read_volume4DROI.

Thanks for helping !

Matthieu

2013/12/12 Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>

Hello experts,

I am running the ball-and-stick model fit in Tracula on FS 5.1 and come across the error: 

WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri
subjectdir is /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_pre: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator
Queuing parallel processing stage
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x66: unexpected operator
Queuing post processing stage
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 216: [: SGE: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 263: [: SGE: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 321: [: xbedpostx_post: unexpected operator
/home/global//freesurfer5.1//bin/fsl_sub_seychelles: 351: [: x: unexpected operator

Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/monitor to show progress.
Type /home/matthieu/NAS/matthieu/DTI_Alex/AR28/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.


I have attached my dmrirc file and trac-all.log.

Best regards,

Matthieu