Hi

Do you have access to a cluster or you run bedpostx on a desktop?
 
Can you also post the output of 

bedpostx_datacheck Dir 
 
where Dir is the name of your input directory? Notice that the Input Directory should contain the 4 files described on http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fdt/UserGuide#BEDPOSTX

Cheers
Stam





On 2 Jul 2013, at 15:42, Andrew James wrote:

> Hello FSL,
> I have encountered difficulties bedposting data, and appreciate any advice you can offer. In summary, when I attempt to bedpost using the GUI, bedposting ends after 10 seconds without producing results. When I attempt to bedpost from the command line, bedposting runs indefinitely without producing results.
> 
> (A) When I attempt to bedpost using the GUI (FSL 5.0.4, using tutorial data) and default parameters (fibres=2, weight=1, burn in=1000), FDT runs for about 10 seconds before displaying "0 slices processed." and the "Done" pop-up message. However, there is no data in the .bedpostx directory.  
> 
> While running, the command line displays the following:
> 
> switching from /home/ajames/dti/gui to /home/ajames/dti/gui
> bedpostx /home/ajames/dti/gui/. --nf=2 --fudge=1  --bi=1000
> /usr/local/fsl/bin/bedpostx /home/ajames/dti/gui/. --nf=2 --fudge=1  --bi=1000
> subjectdir is /home/ajames/dti/gui
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> Queuing post processing stage
> 
> Type /home/ajames/dti/gui.bedpostX/monitor to show progress.
> Type /home/ajames/dti/gui.bedpostX/cancel to terminate all the queued tasks.
> 
> You will get an email at the end of the post-processing stage.
> 
> Done!
> 
> ... and the fslerrorreport reads as follows:
> ERROR: Could not open file
> 
> ######################################################################
> #### MACHINE INFORMATION
> ######################################################################
> 
> Uname:
> Linux
> 
> df:
> Filesystem           1K-blocks      Used Available Use% Mounted on
> /dev/mapper/work-worklv
>                     5160663560 2577201524 2321361152  53% /home
> 
> quota:
> 
> Memory and Swap info:
> MemTotal:     33554432 kB
> MemFree:        454348 kB
> Buffers:        570036 kB
> Cached:       30358108 kB
> SwapCached:          0 kB
> Active:        8821616 kB
> Inactive:     22787576 kB
> HighTotal:           0 kB
> HighFree:            0 kB
> LowTotal:     33554432 kB
> LowFree:        454348 kB
> SwapTotal:     1020116 kB
> SwapFree:      1017036 kB
> Dirty:           88428 kB
> Writeback:           0 kB
> AnonPages:      680792 kB
> Mapped:         145704 kB
> Slab:           615476 kB
> PageTables:      60516 kB
> NFS_Unstable:        0 kB
> Bounce:              0 kB
> CommitLimit:  17797332 kB
> Committed_AS:  2427720 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed:      3236 kB
> VmallocChunk: 34359735095 kB
> 
> ######################################################################
> #### ENVIRONMENT INFORMATION
> ######################################################################
> 
> FSLMULTIFILEQUIT=TRUE
> FSLMACHTYPE=linux_64-gcc4.1
> FSLTCLSH=/usr/local/fsl/bin/fsltclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLWISH=/usr/local/fsl/bin/fslwish
> FSLCONFDIR=/usr/local/fsl/config
> FSLDIR=/usr/local/fsl
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI_GZ
> 
> LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
> PATH=/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/dtk:/usr/local/AFNI/linux_xorg7_64:/usr/local/AFNI/linux_xorg7_64:/usr/local/fsl/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/ajames/bin
> LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
> 
> ######################################################################
> #### DIRECTORY INFORMATION
> ######################################################################
> 
> PWD:
> /home/ajames/dti/gui
> 
> total 109968
> drwxrwxr-x 2 ajames birc      4096 Jul  1 14:36 .
> drwxrwxr-x 6 ajames birc      4096 Jul  1 14:36 ..
> -rw-rw-r-- 1 ajames birc        60 Jul  1 14:36 bedpostcom_log.tcl
> -rwxr-xr-x 1 ajames birc      1041 Jul  1 14:35 bvals
> -rwxr-xr-x 1 ajames birc      2988 Jul  1 14:35 bvecs
> -rwxr-xr-x 1 ajames birc 110756192 Jul  1 14:35 data.nii
> -rw-r--r-- 1 ajames birc   1704288 Jul  1 14:35 nodif_brain_mask.nii
> 
> ######################################################################
> #### IMAGE INFORMATION
> ######################################################################
> 
> 
> This error report is saved in the file: /tmp/fsl_iT7iNF.gz
> 
> (B) When I attempt to bedpost using the command line (using command "bedpostx /home/ajames/dti/commandline/ -n 1", all default options), the bedposting runs indefinitely with no results. After 3 days, the monitor command still reads "0 slices processed."
> 
> When I run fslerrorreport, I get this message:
> /usr/local/fsl/bin/fslerrorreport: line 232: /usr/local/fsl/bin/bedpost_datacheck: No such file or directory
> 
> ######################################################################
> #### MACHINE INFORMATION
> ######################################################################
> 
> Uname:
> Linux
> 
> df:
> Filesystem           1K-blocks      Used Available Use% Mounted on
> /dev/mapper/work-worklv
>                     5160663560 2576385512 2322177164  53% /home
> 
> quota:
> 
> Memory and Swap info:
> MemTotal:     33554432 kB
> MemFree:        919644 kB
> Buffers:        624452 kB
> Cached:       30014452 kB
> SwapCached:          0 kB
> Active:       16034928 kB
> Inactive:     15114520 kB
> HighTotal:           0 kB
> HighFree:            0 kB
> LowTotal:     33554432 kB
> LowFree:        919644 kB
> SwapTotal:     1020116 kB
> SwapFree:      1017036 kB
> Dirty:              32 kB
> Writeback:           0 kB
> AnonPages:      510248 kB
> Mapped:         125964 kB
> Slab:           614140 kB
> PageTables:      54932 kB
> NFS_Unstable:        0 kB
> Bounce:              0 kB
> CommitLimit:  17797332 kB
> Committed_AS:  2169488 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed:      3236 kB
> VmallocChunk: 34359735095 kB
> 
> ######################################################################
> #### ENVIRONMENT INFORMATION
> ######################################################################
> 
> FSLMULTIFILEQUIT=TRUE
> FSLMACHTYPE=linux_64-gcc4.1
> FSLTCLSH=/usr/local/fsl/bin/fsltclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLWISH=/usr/local/fsl/bin/fslwish
> FSLCONFDIR=/usr/local/fsl/config
> FSLDIR=/usr/local/fsl
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI_GZ
> 
> LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
> PATH=/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/dtk:/usr/local/AFNI/linux_xorg7_64:/usr/local/AFNI/linux_xorg7_64:/usr/local/fsl/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/ajames/bin
> LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64
> 
> ######################################################################
> #### DIRECTORY INFORMATION
> ######################################################################
> 
> PWD:
> /home/ajames/dti/commandline.bedpostX
> 
> total 40
> drwxrwxr-x 5 ajames birc 4096 Jul  1 14:43 .
> drwxrwxr-x 8 ajames birc 4096 Jul  1 14:43 ..
> -rwxrwxr-x 1 ajames birc   39 Jul  1 14:43 cancel
> -rw-rw-r-- 1 ajames birc 9270 Jul  1 14:43 commands.txt
> drwxrwxr-x 2 ajames birc 4096 Jul  1 14:43 diff_slices
> drwxrwxr-x 3 ajames birc 4096 Jul  1 14:43 logs
> -rwxrwxr-x 1 ajames birc  621 Jul  1 14:43 monitor
> drwxrwxr-x 2 ajames birc 4096 Jul  1 14:43 xfms
> 
> ######################################################################
> #### FDT INFORMATION
> ######################################################################
> 
> ######################################################################
> #### Main directory:
> 
> total 40
> drwxrwxr-x 5 ajames birc 4096 Jul  1 14:43 .
> drwxrwxr-x 8 ajames birc 4096 Jul  1 14:43 ..
> -rwxrwxr-x 1 ajames birc   39 Jul  1 14:43 cancel
> -rw-rw-r-- 1 ajames birc 9270 Jul  1 14:43 commands.txt
> drwxrwxr-x 2 ajames birc 4096 Jul  1 14:43 diff_slices
> drwxrwxr-x 3 ajames birc 4096 Jul  1 14:43 logs
> -rwxrwxr-x 1 ajames birc  621 Jul  1 14:43 monitor
> drwxrwxr-x 2 ajames birc 4096 Jul  1 14:43 xfms
> 
> 
> This error report is saved in the file: /tmp/fsl_xyx5Gj.gz
> 
> 
> (C) I noticed in the command line fslerrorreport:
> /usr/local/fsl/bin/fslerrorreport: line 232: /usr/local/fsl/bin/bedpost_datacheck: No such file or directory
> 
> Checking the /usr/local/fsl/bin/ directory, I have a bedpostx_datacheck file but not a bedpost_datacheck. Could this be an incomplete installation issue?. I am new to FSL and could not get bedposting to work using v4.something, so I upgraded last week to v5.0.4 (running the self-install from root). How can I check that I have all the necessary files - and if not, replace them?
> 
> Strangely, everything else works. We can process data up to bedposting, and we can process pre-bedposted data to completion. But this step keeps failing.
> 
> Thank you,
> Andy James
>