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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