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Merge pull request #143 from khanlab/warps-rmfullgrid
- adds rules for composite warps from unfold and remove map to full grid
- added a rule to create the ref space for warp files in native space
(similarly to what we already do for unfold space)
- moved ref vols to the seg_{modality} dir (were improperly sitting in the root
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| rule create_native_coord_ref: | ||
| input: | ||
| coords_ap = bids(root='work',datatype='seg_{modality}',dir='AP',suffix='coords.nii.gz',desc='laplace',space='corobl',hemi='{hemi}', **config['subj_wildcards']), | ||
| output: | ||
| nii = bids(root='work',datatype='seg_{modality}',space='corobl',hemi='{hemi}',suffix='refcoords.nii.gz',**config['subj_wildcards']) | ||
| group: 'subj' | ||
| container: config['singularity']['autotop'] | ||
| shell: | ||
| 'c3d {input} -cmp -omc {output}' | ||
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| rule create_warps: | ||
| input: | ||
| unfold_ref_nii = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refvol.nii.gz',**config['subj_wildcards']), | ||
| unfold_phys_coords_nii = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refcoords.nii.gz',**config['subj_wildcards']), | ||
| coords_ap = bids(root='work',datatype='seg_{modality}',dir='AP',suffix='coords.nii.gz',desc='laplace',space='corobl',hemi='{hemi}', **config['subj_wildcards']), | ||
| coords_pd = bids(root='work',datatype='seg_{modality}',dir='PD',suffix='coords.nii.gz',desc='laplace',space='corobl',hemi='{hemi}', **config['subj_wildcards']), | ||
| coords_io = get_laminar_coords, | ||
| native_ref_coords_nii = bids(root='work',datatype='seg_{modality}',space='corobl',hemi='{hemi}',suffix='refcoords.nii.gz',**config['subj_wildcards']) | ||
| params: | ||
| interp_method = 'linear' | ||
| resources: | ||
| mem_mb = 16000 | ||
| output: | ||
| warp_unfold2native = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi,Lflip|R}',from_='unfold',to='corobl',mode='surface'), | ||
| warp_native2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi,Lflip|R}',from_='corobl',to='unfold',mode='surface'), | ||
| warpitk_unfold2native = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi,Lflip|R}',from_='unfold',to='corobl',mode='image'), | ||
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| warpitk_native2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi,Lflip|R}',from_='corobl',to='unfold',mode='image') | ||
| group: 'subj' | ||
| log: bids(root='logs',**config['subj_wildcards'],hemi='{hemi,Lflip|R}',modality='seg-{modality}',suffix='create_warps.txt') | ||
| script: '../scripts/create_warps.py' | ||
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| rule compose_warps_corobl2unfold_lhemi: | ||
| """ Compose corobl to unfold (unfold-template), for left hemi (ie with flip)""" | ||
| input: | ||
| native2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='Lflip',from_='corobl',to='unfold',mode='image'), | ||
| ref = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refvol.nii.gz',**config['subj_wildcards']), | ||
| flipLR_xfm = os.path.join(config['snakemake_dir'],'resources','desc-flipLR_type-itk_xfm.txt') | ||
| output: | ||
| corobl2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='L',from_='corobl',to='unfold',mode='image') | ||
| container: config['singularity']['autotop'] | ||
| group: 'subj' | ||
| shell: 'ComposeMultiTransform 3 {output.corobl2unfold} -R {input.ref} {input.native2unfold} {input.flipLR_xfm}' | ||
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| #consider renaming to state this composition is to "un-flip" | ||
| rule compose_warps_unfold2corobl_lhemi: | ||
| """ Compose unfold (unfold-template) to corobl, for left hemi (ie with flip)""" | ||
| input: | ||
| unfold2native = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='Lflip',from_='unfold',to='corobl',mode='image'), | ||
| flipLR_xfm = os.path.join(config['snakemake_dir'],'resources','desc-flipLR_type-itk_xfm.txt'), | ||
| unfold_ref = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refvol.nii.gz',**config['subj_wildcards']), | ||
| ref = bids(root='work',datatype='seg_{modality}',dir='AP',suffix='coords.nii.gz',desc='laplace',space='corobl',hemi='L', **config['subj_wildcards']), | ||
| output: | ||
| unfold2corobl = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='L',from_='unfold',to='corobl',mode='image') | ||
| container: config['singularity']['ants'] | ||
| group: 'subj' | ||
| shell: 'antsApplyTransforms -o [{output.unfold2corobl},1] -r {input.ref} -t {input.flipLR_xfm} -t {input.unfold2native} -i {input.unfold_ref} -v' | ||
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| rule compose_warps_t1_to_unfold: | ||
| """ Compose warps from T1w to unfold """ | ||
| input: | ||
| corobl2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='corobl',to='unfold',mode='image'), | ||
| ref = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refvol.nii.gz',**config['subj_wildcards']), | ||
| t1w2corobl = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='xfm.txt',from_='T1w',to='corobl',desc='affine',type_='itk'), | ||
| output: | ||
| bids(root='results',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='T1w',to='unfold',mode='image') | ||
| container: config['singularity']['ants'] | ||
| group: 'subj' | ||
| shell: 'ComposeMultiTransform 3 {output} -R {input.ref} {input.corobl2unfold} {input.t1w2corobl}' | ||
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| rule compose_warps_unfold_to_cropt1: | ||
| """ Compose warps from unfold to cropT1w """ | ||
| input: | ||
| unfold2corobl = bids(root='results',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='unfold',to='corobl',mode='image'), | ||
| ref = bids(root='work',datatype='seg_{modality}',suffix='cropref.nii.gz', space='T1w',hemi='{hemi}', **config['subj_wildcards']), | ||
| t1w2corobl = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='xfm.txt',from_='T1w',to='corobl',desc='affine',type_='itk'), | ||
| unfold_ref = bids(root='work',space='unfold',datatype='seg_{modality}',suffix='refvol.nii.gz',**config['subj_wildcards']), | ||
| output: | ||
| unfold2cropt1 = bids(root='results',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='unfold',to='T1w',mode='image') | ||
| container: config['singularity']['ants'] | ||
| group: 'subj' | ||
| shell: 'antsApplyTransforms -o [{output.unfold2cropt1},1] -r {input.ref} -t [{input.t1w2corobl},1] -t {input.unfold2corobl} -i {input.unfold_ref} -v' | ||
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