Dear Alan,
Where are your files and what names have you given them?
It sounds like the vbm script is confused about where they are and cannot find them, but I don't know why without having more information.
All the best,
Mark
On 28 Aug 2013, at 18:39, Alan Francis <[log in to unmask]> wrote:
> Hi FSL folk:
>
> I have just begun a VBM analysis on 2 matched groups. These are memprage scans that were RMS ed. When I examined the slices directory the brains looked good. See below
>
> file:///autofs/space/dali_003/users/FSL-VBM/NEW/slicesdir/index.html
>
> However when I ran fslvbm_1_bet -b it gave me an error message :
>
> /autofs/cluster/nrg/tools/0.9.6/apps/arch/linux_x86_64/fsl/4.0.3/bin/fslvbm_1_bet: line 94: cd: FAi: No such file or directory
> *FAi
>
> Error: input image *FAi not valid
>
> *FAi
> ** ERROR (nifti_image_read): failed to find header file for '*FAi'
> ** ERROR: nifti_image_open(*FAi): bad header info
> Error: failed to open file *FAi
> ERROR: Could not open image *FAi
> Image Exception : #22 :: Failed to read volume *FAi
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> /autofs/cluster/nrg/tools/0.9.6/apps/arch/linux_x86_64/fsl/4.0.3/bin/slicesdir: line 132: 44506 Aborted (core dumped) ${FSLDIR}/bin/slicer $A $B -s 1 $sliceropts
>
> Cannot open slicesdir/grota.png for reading
> /autofs/cluster/nrg/tools/0.9.6/apps/arch/linux_x86_64/fsl/4.0.3/bin/slicesdir: line 132: 44514 Segmentation fault (core dumped) ${FSLDIR}/bin/pngappend $convertopts slicesdir/${Q}.png
>
> Finished. To view, point your web browser at
> file:/autofs/space/dali_003/users/FSL-VBM/fsl_vbm/slicesdir/index.html
>
> Any help is deeply appreciated,
>
> thanks,
>
> Alan
>
|