Hi
Can you run:
bedpostx_datacheck /scratch/Massih/Tractography/c_AH
and send us the output?
Cheers,
Saad.
On 13 Aug 2009, at 16:49, Massieh Moayedi wrote:
> Hi,
>
> I was rerunning bedpostx and have run into a bit of a problem. The
> program terminates
> within the first minute. It ran fine last time, but I'm not sure
> what the new error is from.
> I've just upgraded this machine to fsl414.
>
> I've pasted the error report below. Any ideas as to what's going on?
>
> Massih Moayedi
>
> Last login: Thu Aug 13 11:35:31 on ttys000
> -------- freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5 --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: /Applications/freesurfer/subjects/TMD/Patients does not exist
> FREESURFER_HOME /Applications/freesurfer
> FSFAST_HOME /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii
> SUBJECTS_DIR /Applications/freesurfer/subjects/TMD/Patients
> MNI_DIR /Applications/freesurfer/mni
> users/jpoublan [mikulis4.uhnres.utoronto.ca:1]% fsl
> users/jpoublan [mikulis4.uhnres.utoronto.ca:2]% cs //scratch
> cs: Command not found.
> users/jpoublan [mikulis4.uhnres.utoronto.ca:3]% cd //scratch
> /scratch [mikulis4.uhnres.utoronto.ca:4]% cd Massih
> scratch/Massih [mikulis4.uhnres.utoronto.ca:5]% cd Tractography/
> Massih/Tractography [mikulis4.uhnres.utoronto.ca:6]% LS
> LS: Command not found.
> Massih/Tractography [mikulis4.uhnres.utoronto.ca:7]% ls
> c_AH/ c_BF/ c_MPM/ c_RAL/ c_WT/ p_AM/ p_JQ/ p_MCM/ p_SK/
> p_WV/
> c_AO/ c_IT/ c_MW/ c_SF/ p_AGP/ p_GL/ p_KR/ p_MD/ p_SM/
> c_AY/ c_MK/ c_NS/ c_TJ/ p_AHP/ p_JG/ p_MAM/ p_MNM/ p_WM/
> Massih/Tractography [mikulis4.uhnres.utoronto.ca:8]% bedpostx c_AH
> subjectdir is /scratch/Massih/Tractography/c_AH
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> 0 slices processed
> Queuing post processing stage
> /Applications/fsl414/bin/bedpostx: line 220: 30799 Terminated
> ${subjdir}.bedpostX/monitor
> Massih/Tractography [mikulis4.uhnres.utoronto.ca:9]% fslerrorreport
> /Applications/fsl414/bin/fslerrorreport: line 100: vmstat: command
> not found
> ** ERROR (nifti_image_read): failed to find header file for '/
> scratch/Massih/Tractography'
> ** ERROR: nifti_image_open(/scratch/Massih/Tractography): bad header
> info
> Error: failed to open file /scratch/Massih/Tractography
> ERROR: Could not open file
>
> #######################################################
> ###############
> #### MACHINE INFORMATION
> #######################################################
> ###############
>
> Uname:
> Darwin
>
> df:
> Filesystem 512-blocks Used Available Capacity Mounted on
> /dev/disk2s2 1464082352 300125216 1163445136 21% /
>
> quota:
> Disk quotas for user jpoublan (uid 9294): none
>
> Memory and Swap info:
> Mach Virtual Memory Statistics: (page size of 4096 bytes)
> Pages free: 3088706.
> Pages active: 787729.
> Pages inactive: 46835.
> Pages wired down: 269353.
> "Translation faults": 663034381.
> Pages copy-on-write: 27511585.
> Pages zero filled: 3164233196.
> Pages reactivated: 6772.
> Pageins: 395308.
> Pageouts: 134.
> Object cache: 4936165 hits of 67957048 lookups (7% hit rate)
>
> #######################################################
> ###############
> #### ENVIRONMENT INFORMATION
> #######################################################
> ###############
>
> FSLMULTIFILEQUIT=TRUE
> FSLMACHTYPE=apple-darwin9-gcc4.0
> FSLTCLSH=/Applications/fsl414/bin/fsltclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLCONFDIR=/Applications/fsl414/config
> FSLWISH=/Applications/fsl414/bin/fslwish
> FSLDIR=/Applications/fsl414
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI_GZ
>
> MANPATH=/usr/share/man:/usr/local/share/man:/usr/X11/man
> PATH=/Library/Frameworks/Python.framework/Versions/Current/bin:/
> Applications/fsl414/
> bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/
> bin:/Applications/freesurfe
> r/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/
> users/jpoublan/binjul:
> /usr/X11R6/bin:/Applications/freesurfer/bin:/Applications/
> freesurfer//mni/bin/:/Users/jpo
> ublan/mricronmac:/Applications/AFNI:/sw/bin:/users/jpoublan/NONO/wmh-
> linux/FLEX
> MNI_DATAPATH=/Applications/freesurfer/mni/data
>
> #######################################################
> ###############
> #### DIRECTORY INFORMATION
> #######################################################
> ###############
>
> PWD:
> /scratch/Massih/Tractography
>
> total 16
> drwxrwxrwx 31 jpoublan mri 1054 13 Aug 11:42 .
> drwxrwxrwx 4 jpoublan admin 136 13 Aug 11:35 ..
> -rw-rw-rw-@ 1 jpoublan mri 6148 13 Aug 11:42 .DS_Store
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:12 c_AH
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:13 c_AO
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:13 c_AY
> drwxrwxrwx 7 jpoublan mri 238 12 Aug 08:53 c_BF
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:13 c_IT
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:13 c_MK
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:14 c_MPM
> drwxrwxrwx 7 jpoublan mri 238 12 Aug 08:54 c_MW
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:13 c_NS
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:14 c_RAL
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:15 c_SF
> drwxrwxrwx 7 jpoublan mri 238 12 Aug 08:55 c_TJ
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:15 c_WT
> drwxrwxrwx 113 jpoublan mri 3842 13 Aug 10:16 p_AGP
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:17 p_AHP
> drwxrwxrwx 7 jpoublan mri 238 12 Aug 08:56 p_AM
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:16 p_GL
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:16 p_JG
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:17 p_JQ
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:18 p_KR
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:16 p_MAM
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:17 p_MCM
> drwxrwxrwx 113 jpoublan mri 3842 13 Aug 10:17 p_MD
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:18 p_MNM
> drwxrwxrwx 113 jpoublan mri 3842 13 Aug 10:16 p_SK
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:17 p_SM
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:18 p_WM
> drwxrwxrwx 117 jpoublan mri 3978 13 Aug 10:18 p_WV
>
> #######################################################
> ###############
> #### IMAGE INFORMATION
> #######################################################
> ###############
>
>
> This error report is saved in the file: /tmp/fsl_VtAZk8.gz
>
> Massih/Tractography [mikulis4.uhnres.utoronto.ca:10]% fsl
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222523 (fax 717)
www.fmrib.ox.ac.uk/~saad
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