Hi Steve,
Might be clearer if I show you the script I'm running:
># !/bin/bash
>#
>#
># ./process_dti.txt directory dti_filename dwi_filename n_slices
>n_directions_including_B0
>#
># $1: dir: full data directory
># $2: dti_fname: Philips raw images assumes .REC extension, in $1/raw
># $3: dwi_fname: Philips raw images assumes .REC extension, in $1/raw
># dwi has two frames only
># $4: number of slices
># $5: total number of frames in dti file
>#
># output is $3.img, $3.hdr in $1/processed
>#
>pwdor=`pwd`
>mkdir "$1"/processed
>cd "$1"/processed
>/bin/rm -r -f t*
>fslcreatehd 128 128 2 "$4" 1.75 1.75 2.0 2.0 0.0 0.0 0.0 4 ttt1
>cp ../raw/"$3".REC ttt1.img
>fslsplit ttt1
>fslcreatehd 128 128 1 2 1.75 1.75 2.0 2.0 0.0 0.0 0.0 4 ttt2
..... then there's more, but this is where things go wrong.
I'm creating a .img file, but then the fslsplit command creates .nii.gz files.
I'm scratching my head now because I've changed the default formats as per
the help and it apparently hasn't actually done anything.
I've changed the default file format in ${FSLDIR}/etc/fslconf/ and created a
.fslconf directory and changed the file format to ANALYZE there as well.
Still no luck though....
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