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| Original file line number | Diff line number | Diff line change |
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| # WIP - workflow for updating atlases to new v2 specs | ||
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| This example is run from the existing multihist atlas folder. | ||
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| Still needs updates for cifti structure labels etc (will add this in once we have an updated wb_command/wb_view in our deps) | ||
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| We currently have templates and atlases in hippunfold (selected by --template and --atlas), where the former selects the volume-based template used for volumetric registration, and the latter selects the unfolded-space subfields (and metrics for unfolded registration). I am proposing the latter become purely surface-based, so instead of providing labels and metrics in the volumetric unfolded space, we use giftis for everything, and this now becomes surface-templates instead of atlases. |
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| Original file line number | Diff line number | Diff line change |
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| hippunfold_dir = "/localscratch/hippunfold_khanlab" | ||
| hipp_dseg = "sub-maxprob_label-hipp_desc-manualsubfieldsunfoldaligned_dseg.nii.gz" | ||
| labellist = "labellist_withdg.txt" | ||
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| hemis = ["L", "R"] | ||
| metrics = ["thickness", "curvature", "gyrification"] | ||
| surftypes = ["midthickness", "inner", "outer"] | ||
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| hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"} | ||
| surf_to_secondary_type = { | ||
| "midthickness": "MIDTHICKNESS", | ||
| "inner": "PIAL", | ||
| "outer": "GRAY_WHITE", | ||
| } | ||
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| rule all: | ||
| input: | ||
| expand( | ||
| "hemi-{hemi}_label-{label}_dseg.label.gii", | ||
| label=["hipp", "dentate"], | ||
| hemi=hemis, | ||
| ), | ||
| expand( | ||
| "hemi-{hemi}_label-{label}_{metric}.shape.gii", | ||
| label=["hipp"], | ||
| hemi=hemis, | ||
| metric=metrics, | ||
| ), | ||
| expand( | ||
| "hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii", | ||
| label=["hipp", "dentate"], | ||
| hemi=hemis, | ||
| surftype=surftypes, | ||
| ), | ||
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| rule hipp_dseg: | ||
| input: | ||
| hipp_dseg, | ||
| output: | ||
| temp("hipp_dseg.nii.gz"), | ||
| shell: | ||
| "cp {input} {output}" | ||
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| rule dentate_dseg: | ||
| input: | ||
| hipp_dseg, | ||
| params: | ||
| dg_label=6, | ||
| output: | ||
| temp("dentate_dseg.nii.gz"), | ||
| shell: | ||
| "c3d {input} -scale 0 -shift {params.dg_label} -o {output}" | ||
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| rule surf_gifti: | ||
| input: | ||
| surf_gii=Path(hippunfold_dir) | ||
| / "hippunfold" | ||
| / "resources" | ||
| / "unfold_template_{label}" | ||
| / "tpl-avg_space-unfold_den-unfoldiso_{surftype}.surf.gii", | ||
| params: | ||
| structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi], | ||
| secondary_type=lambda wildcards: surf_to_secondary_type[wildcards.surftype], | ||
| surface_type="FLAT", | ||
| output: | ||
| surf_gii="hemi-{hemi}_space-unfold_label-{label}_{surftype}.surf.gii", | ||
| shell: | ||
| "cp {input} {output} && " | ||
| "wb_command -set-structure {output} {params.structure_type} -surface-type {params.surface_type}" | ||
| " -surface-secondary-type {params.secondary_type}" | ||
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| rule label_gifti: | ||
| input: | ||
| dseg_nii="{label}_dseg.nii.gz", | ||
| lut=labellist, | ||
| surf_gii="hemi-{hemi}_space-unfold_label-{label}_midthickness.surf.gii", | ||
| params: | ||
| structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi], | ||
| output: | ||
| label_gii="hemi-{hemi}_label-{label}_dseg.label.gii", | ||
| shadow: | ||
| "minimal" | ||
| shell: | ||
| "wb_command -volume-label-import {input.dseg_nii} {input.lut} label_vol.nii && " | ||
| "wb_command -volume-label-to-surface-mapping label_vol.nii {input.surf_gii} {output.label_gii} && " | ||
| "wb_command -set-structure {output} {params.structure_type}" | ||
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| rule metric_gifti: | ||
| input: | ||
| metric_nii="{metric}.nii.gz", | ||
| surf_gii="hemi-{hemi}_space-unfold_label-{label}_inner.surf.gii", #existing metric niftis are on inner space | ||
| params: | ||
| structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi], | ||
| output: | ||
| metric_gii="hemi-{hemi}_label-{label}_{metric}.shape.gii", | ||
| shadow: | ||
| "minimal" | ||
| shell: | ||
| "wb_command -volume-to-surface-mapping {input.metric_nii} {input.surf_gii} {output.metric_gii} -trilinear && " | ||
| "wb_command -set-structure {output} {params.structure_type}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Subiculum | ||
| 1 0 0 255 255 | ||
| CA1 | ||
| 2 133 222 255 255 | ||
| CA2 | ||
| 3 0 255 170 255 | ||
| CA3 | ||
| 4 255 162 0 255 | ||
| CA4 | ||
| 5 255 0 0 255 | ||
| DG | ||
| 6 255 255 0 255 |
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