Hi,
I take it you're not trying to use SGE or a cluster environment, but
just running on a single computer?
You don't need to install a license for the IRTK binaries. Did you put
them in $FSLDIR/bin/DR ?
There may be some *.o* or *.e* log files in FAi. What do they say?
There's no point going on to run tbss_3_postreg if tbss_2_reg has
failed.
Cheers, Steve.
On 14 Feb 2008, at 10:06, Filippo Panessa wrote:
> Hi,
> I'm an IT from the University of Rome (La Sapienza) and actually I'm
> working
> at the department of neurology. We've got a lot of trouble using fsl
> (expecially the tbss software). I have tried to set up tbss on
> debian (etch
> and lenny) and ubuntu (feisty and gutsy) using official and unofficial
> packages (Michael Hanke).
>
> In every machine (32 bit) we have:
>
> - fsl package from your repository
> - fsl-atlases from your repository
> - fslview from your repository
> - itk manually dowloaded and installed under /usr/local
> - . /ect/fsl/fsl.sh globally set in /etc/bash.bashrc
> - itk binaries in PATH (should we need a license for this ?)
> - /bin/sh is a symbolic link to /bin/bash (NOT dash)
>
> tbss_1_preproc CON_N00300_dti_data_FA.nii.gz
> CON_N00302_dti_data_FA.nii.gz
> seems to work (it creates hdr and img files under FAi directory and
> moves
> nii files under origdata).
>
> tbss_2_reg -T seems to have problems (the process runs just for few
> seconds
> and two empty msf files are created under FAi directory:
> CON_N00300_dti_data_FA_FAi_to_target_nonlinear.msf and
> CON_N00302_dti_data_FA_FAi_to_target_nonlinear.msf).
>
> Finally, tbss_3_postreg -S crashes with this output:
>
> /usr/lib/fsl/tbss_3_postreg: line 96: cd: FAi: No such file or
> directory
> using pre-chosen target for registration
> transforming all FA images into MNI152 space
> CON_N00300_dti_data_FA_FAi
> ** ERROR (nifti_image_read): failed to find header file for
> 'CON_N00300_dti_data_FA_FAi_to_target_nonlinear'
> ** ERROR:
> nifti_image_open(CON_N00300_dti_data_FA_FAi_to_target_nonlinear):
> bad header info
> Error: failed to open file
> CON_N00300_dti_data_FA_FAi_to_target_nonlinear
> ERROR: Could not open image
> CON_N00300_dti_data_FA_FAi_to_target_nonlinear
> Image Exception : #22 :: Failed to read volume
> CON_N00300_dti_data_FA_FAi_to_target_nonlinear
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/lib/fsl/tbss_3_postreg: line 148: 11552 Abortito
> $FSLDIR/bin/applywarp -i $f -o ${f}_to_target_nonlinear_hr -r target
> -w
> ${f}_to_target_nonlinear --rel
> CON_N00302_dti_data_FA_FAi
> ** ERROR (nifti_image_read): failed to find header file for
> 'CON_N00302_dti_data_FA_FAi_to_target_nonlinear'
> ** ERROR:
> nifti_image_open(CON_N00302_dti_data_FA_FAi_to_target_nonlinear):
> bad header info
> Error: failed to open file
> CON_N00302_dti_data_FA_FAi_to_target_nonlinear
> ERROR: Could not open image
> CON_N00302_dti_data_FA_FAi_to_target_nonlinear
> Image Exception : #22 :: Failed to read volume
> CON_N00302_dti_data_FA_FAi_to_target_nonlinear
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/lib/fsl/tbss_3_postreg: line 148: 11553 Abortito
> $FSLDIR/bin/applywarp -i $f -o ${f}_to_target_nonlinear_hr -r target
> -w
> ${f}_to_target_nonlinear --rel
> merging all upsampled FA images into single 4D image
>
> Usage: fslmerge <-x/y/z/t/a> <output> <file1 file2 .......>
> -t : concatenate images in time
> -x : concatenate images in the x direction
> -y : concatenate images in the y direction
> -z : concatenate images in the z direction
> -a : auto-choose: single slices -> volume, volumes -> 4D (time
> series)
> ** ERROR (nifti_image_read): failed to find header file for 'all_FA'
> ** ERROR: nifti_image_open(all_FA): bad header info
> Error: failed to open file all_FA
> Error:: FslCloneHeader: Null pointer passed for FSLIO
> creating valid mask and mean FA
> ** ERROR (nifti_image_read): failed to find header file for 'all_FA'
> ** ERROR: nifti_image_open(all_FA): bad header info
> Error: failed to open file all_FA
> Cannot open volume all_FA for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'all_FA'
> ** ERROR: nifti_image_open(all_FA): bad header info
> Error: failed to open file all_FA
> Cannot open volume all_FA for reading!
> ** ERROR (nifti_image_read): failed to find header file for 'all_FA'
> ** ERROR: nifti_image_open(all_FA): bad header info
> Error: failed to open file all_FA
> Cannot open volume all_FA for reading!
> skeletonising mean FA
> ** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
> ** ERROR: nifti_image_open(mean_FA): bad header info
> Error: failed to open file mean_FA
> ERROR: Could not open image mean_FA
> Image Exception : #22 :: Failed to read volume mean_FA
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/lib/fsl/tbss_3_postreg: line 190: 11588 Abortito
> $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
> now view mean_FA_skeleton to check whether the default threshold of
> 2000
> needs changing, when running:
> tbss_4_prestats [threshold]
>
>
> Is this a sort of bug ?
>
> Thank you for your help.
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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