Hi,
Right - this must be a buglet in the script for when you're not using
NIFTI_GZ data format - we'll fix that for the next release.
Cheers.
On 25 Feb 2008, at 16:07, Matthew Kempton wrote:
> Thanks Steve,
>
> So it seems from what you say I should go into the directory
> IMAGE1_to_IMAGE2_siena then type
>
> siena_flow2std A B
>
> This appears to work. The only small issue is that when the debug
> mode is
> not selected the files produced are:
>
>
> A_brain.img
> A_to_std.mat
> A_halfwayto_B_to_std.mat
> A_to_std.img
> A_to_B_flow_dil.img
> A_masksmooth.img
> A_to_B_flow_to_std.hdr
> A_to_B_flow_to_std.img
>
> ie A_brain.img, A_to_std.img, A_masksmooth.img
> are all produced without header files. In debug mode (siena_flow2std
> A B -
> d) the headers are produced.
>
> It seems this happens because the cleanup section of the script reads
>
> if [ $debug = 0 ] ; then
>
> /bin/rm -f ${A}_halfwayto_${B}_inv.mat `$FSLDIR/bin/imglob -
> oneperimage
> ${A}_masksmooth ${A}_brain.* ${A}_to_${B}_flow_dil.* ${A}_to_std.*`
>
> Because the -oneperimage flag is specified only the header files are
> deleted.
>
>
> Matthew Kempton
> Institute of Psychiatry
> London
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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