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- #!/bin/tcsh
- # AFIDS_template_xalign.csh
- # make swarm script for SLURM processing
- #
- # list of templates to align to each other
- set template_list = ( NMT_v2.0_sym_SS.nii.gz \
- NMT_v2.1_asym_SS.nii.gz \
- NMT_1.3_SS.nii.gz \
- D99.nii.gz \
- inia19.nii \
- yerkes19.nii.gz \
- macMNI_rescale.nii.gz \
- )
- # some short names to match the list of templates in order
- set template_abbrev_list = ( NMTv2sym NMTv2asym NMTv1.3 D99 inia19 Yerkes19 MNImac )
- set template_index = 1
- # remove previous swarm script
- rm aw_all_cmds.swarm
- # warp all templates to all the other templates
- # avoid duplication by not repeating previous templates
- foreach template ( $template_list )
- # make the base to align to start at the next in the list
- set templatebase_index = `ccalc -int "$template_index+1" `
- foreach templatebase ( ${template_list[${templatebase_index}-]} )
- set aw_cmd = "@animal_warper -ok_to_exist \
- -base $templatebase \
- -base_abbrev ${template_abbrev_list[$templatebase_index]} \
- -input ${template_list[$template_index]} \
- -input_abbrev ${template_abbrev_list[$template_index]} \
- -outdir aw_${template_abbrev_list[$template_index]}_to_${template_abbrev_list[$templatebase_index]}"
- echo $aw_cmd >> aw_all_cmds.swarm
- @ templatebase_index ++
- end
- @ template_index ++
- end
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