JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  August 2009

FSL August 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

bedpostx doesn't run

From:

Massieh Moayedi <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 13 Aug 2009 16:49:12 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (156 lines)

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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager