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
