Dear SIENA experts,
For a group study of longitudinal brain changes I am trying to run
multiple SIENAs in a script. To get better results than standard BET I
would like to pass the " -R " option to SIENA.
The current version of the scripts generates the SIENA calls in this loop:
> ...
> for f in ${new1999}/f*.nii.gz; do
> studyID=`basename ${f%%.nii*}`
> studyID=${studyID:1}
> sienadir=${cwd}/longit/siena_${studyID}
> mkdir -p ${sienadir}
> CM="siena ${new1999}/f${studyID}.nii.gz
> ${new2009}/f${studyID}.nii.gz -o ${sienadir} -d -B \" -R \""
> echo ${CM}
> ${CM}
> done
> ...
The output of the script is
> siena data1999/f00001.nii.gz data2009/f00001.nii.gz -o
> longit/siena_00001 -d -o longit/siena_00001 -d -B " -R "
>
> Usage: siena <input1> <input2> [options]
> -o <output-dir> : set output directory (default output is
> <input1>_to_<input2>_siena)
> -d : debug (don't delete intermediate files)
> -B "betopts" : options to pass to BET brain extraction
> (inside double-quotes), e.g. -B "-f 0.3"
> -2 : two-class segmentation (don't segment grey
> and white matter separately)
> -t2 : T2-weighted input image (default T1-weighted)
> -m : use standard-space masking as well as BET
> -t <t> : ignore from t (mm) upwards in
> MNI152/Talairach space
> -b <b> : ignore from b (mm) downwards in
> MNI152/Talairach space (b should probably be negative)
> -S "sienadiffopts" : options to pass to siena_diff timepoint
> differencing (inside double-quotes), e.g. -S "-s -i 20"
> ... et cetera for other subjects
So even though it seems that the correct command line ${CM} is created,
calling the command results in an error.
Has anyone else tried to use a script to generate SIENA calls (an
succeeded)? Or is the use of " -R " not a good idea in the first place?
Thanks,
Alle Meije Wink
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