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

Hi Matthieu - This error had to do with a change in bedpostx's command line arguments after an FSL upgrade. The problem is fixed in the newer version of tracula. Again, I'd strongly recommend upgrading to the newer tracula.

Hope this helps, a.y

On Thu, 12 Dec 2013, Matthieu Vanhoutte wrote:

Hello experts,

I am running the ball-and-stick model fit in Tracula on FS 5.1 and come acro ss 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 o perator 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: unex pected 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 o perator

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 termi nate 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