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fix tbss_non_FA to match FSL's tbss_non_FA command
Here is the FSL command from their source code:
"${FSLDIR}/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${ALTIM}skeletonised -a all$ALTIM"
where all_${ALTIM} in my example is all_RD. notice all_FA is in the placeholder for the 4d Data file under the -p option, and the -a all_RD is there too.
here is what I changed in tbss.py to allow for this:
see new inputnode, all_FA_file and
see (maskgroup, projectfa, [('out_file', 'alt_data_file')]) step in tbss_non_fa.connect command. This is to get the -a option with the all_RD file.
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