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merged spec files, fix for copying results
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also moves refvol to work folder, so should have no warps directory now (as
it is not really needed)..
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@akhanf
akhanf committed Jan 10, 2025
1 parent c9ac98b commit 3cd2053
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Showing 4 changed files with 148 additions and 74 deletions.
38 changes: 5 additions & 33 deletions hippunfold/workflow/rules/common.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,36 +48,11 @@ def get_final_spec():
datatype="surf",
den="{density}",
space="{space}",
hemi="{hemi}",
label="{autotop}",
suffix="surfaces.spec",
**inputs.subj_wildcards,
),
density=config["output_density"],
space=ref_spaces,
hemi=config["hemi"],
autotop=config["autotop_labels"],
surfname=config["surf_types"]["hipp"],
allow_missing=True,
)
)
specs.extend(
inputs[config["modality"]].expand(
bids(
root=root,
datatype="surf",
den="{density}",
space="{space}",
hemi="{hemi}",
label="{autotop}",
suffix="surfaces.spec",
**inputs.subj_wildcards,
),
density=config["output_density"],
space=ref_spaces,
hemi=config["hemi"],
autotop=config["autotop_labels"],
surfname=config["surf_types"]["dentate"],
allow_missing=True,
)
)
Expand All @@ -87,15 +62,10 @@ def get_final_spec():
root=root,
datatype="surf",
space="{space}",
hemi="{hemi}",
label="{autotop}",
suffix="surfaces.spec",
**inputs.subj_wildcards,
),
space="corobl",
hemi=config["hemi"],
autotop=config["autotop_labels"],
surfname=config["surf_types"]["hipp"],
allow_missing=True,
)
)
Expand Down Expand Up @@ -306,7 +276,7 @@ if "corobl" in ref_spaces:
input:
os.path.join(work, "{pre}_space-corobl_{post}{suffix}.{ext}"),
output:
os.path.join(root, "{pre}_space-corobl_{post}{suffix,coords}.{ext}"),
os.path.join(root, "{pre,[^/].+}_space-corobl_{post}{suffix,coords}.{ext}"),
group:
"subj"
shell:
Expand All @@ -316,7 +286,9 @@ if "corobl" in ref_spaces:
input:
os.path.join(work, "{pre}_{fromto,from|to}-corobl_{post}{suffix}.{ext}"),
output:
os.path.join(root, "{pre}_{fromto,from|to}-corobl_{post}{suffix,xfm}.{ext}"),
os.path.join(
root, "{pre,[^/].+}_{fromto,from|to}-corobl_{post}{suffix,xfm}.{ext}"
),
group:
"subj"
shell:
Expand All @@ -326,7 +298,7 @@ if "corobl" in ref_spaces:
input:
os.path.join(work, "{pre}_desc-subfields_{post}{suffix}.{ext}"),
output:
os.path.join(root, "{pre}_desc-subfields_{post}{suffix,dseg}.{ext}"),
os.path.join(root, "{pre,[^/].+}_desc-subfields_{post}{suffix,dseg}.{ext}"),
group:
"subj"
shell:
Expand Down
58 changes: 49 additions & 9 deletions hippunfold/workflow/rules/gifti.smk
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
# lookup tables for structure:
hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}


# lookup mappings for structure and surface type:
def get_structure(hemi, label):
if label == "hipp":
if hemi == "L":
Expand Down Expand Up @@ -123,7 +120,7 @@ rule constrain_surf_to_bbox:
**inputs.subj_wildcards
),
ref_nii=bids(
root=root,
root=work,
datatype="warps",
space="unfold",
label="{autotop}",
Expand Down Expand Up @@ -335,7 +332,7 @@ rule create_dlabel_cifti_subfields:
def get_cmd_spec_file(wildcards, input, output):
specfile = output.spec_file
if "hemi" in wildcards._names:
structure = hemi_to_structure[wildcards.hemi]
structure = get_structure(wildcards.hemi, wildcards.label)
else:
structure = "INVALID"
cmds = list()
Expand Down Expand Up @@ -519,7 +516,14 @@ rule create_spec_file_dentate:
"{params.cmds}"


rule merge_lr_spec_file:
def get_cmd_merge_spec(wildcards, input, output):
if len(input.spec_files) == 1:
return f"cp {input} {output}"
else:
return f"wb_command -spec-file-merge {input.spec_files} {output}"


rule merge_lr_spec_file_native:
input:
spec_files=expand(
bids(
Expand All @@ -532,9 +536,11 @@ rule merge_lr_spec_file:
label="{autotop}",
**inputs.subj_wildcards
),
hemi=["L", "R"],
hemi=config["hemi"],
allow_missing=True,
),
params:
cmd=get_cmd_merge_spec,
output:
spec_file=bids(
root=root,
Expand All @@ -550,4 +556,38 @@ rule merge_lr_spec_file:
group:
"subj"
shell:
"wb_command -spec-file-merge {input.spec_files} {output}"
"{params.cmd}"


rule merge_hipp_dentate_spec_file_native:
input:
spec_files=expand(
bids(
root=root,
datatype="surf",
den="{density}",
suffix="surfaces.spec",
space="{space}",
label="{autotop}",
**inputs.subj_wildcards
),
autotop=config["autotop_labels"],
allow_missing=True,
),
params:
cmd=get_cmd_merge_spec,
output:
spec_file=bids(
root=root,
datatype="surf",
den="{density}",
space="{space}",
suffix="surfaces.spec",
**inputs.subj_wildcards
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"{params.cmd}"
118 changes: 90 additions & 28 deletions hippunfold/workflow/rules/native_surf.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -921,7 +921,7 @@ rule pad_unfold_ref:
for this)."""
input:
ref_nii=bids(
root=root,
root=work,
space="unfold",
label="{label}",
datatype="warps",
Expand Down Expand Up @@ -1360,33 +1360,29 @@ rule convert_unfoldreg_warp_from_itk_to_world:
"wb_command -convert-warpfield -from-itk {input} -to-world {output}"


def get_unfold_ref(wildcards):
"""function to return either unfoldreg or unfold ref mesh, depending on whether
unfoldreg can be performed (based on atlas wildcards)"""

def get_unfold_ref_name(wildcards):
if (
wildcards.label in config["atlas_files"][config["atlas"]]["label_wildcards"]
and config["no_unfolded_reg"] == False
):
return bids(
root=root,
datatype="surf",
suffix="midthickness.surf.gii",
space="unfoldreg",
hemi="{hemi}",
label="{label}",
**inputs.subj_wildcards
)
return "unfoldreg"
else:
return bids(
root=root,
datatype="surf",
suffix="midthickness.surf.gii",
space="unfold",
hemi="{hemi}",
label="{label}",
**inputs.subj_wildcards
)
return "unfold"


def get_unfold_ref(wildcards):
"""function to return either unfoldreg or unfold ref mesh, depending on whether
unfoldreg can be performed (based on atlas wildcards)"""

return bids(
root=root,
datatype="surf",
suffix="midthickness.surf.gii",
space=get_unfold_ref_name(wildcards),
hemi="{hemi}",
label="{label}",
**inputs.subj_wildcards
)


rule warp_unfold_native_to_unfoldreg:
Expand Down Expand Up @@ -1623,7 +1619,7 @@ rule atlas_label_to_unfold_nii:
input:
atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
ref_nii=bids(
root=root,
root=work,
space="unfold",
label="{label}",
datatype="warps",
Expand Down Expand Up @@ -1805,7 +1801,7 @@ rule create_spec_file_hipp_native:
atlas=config["atlas"],
allow_missing=True,
),
surfs=expand(
surfs=lambda wildcards: expand(
bids(
root=root,
datatype="surf",
Expand All @@ -1816,7 +1812,7 @@ rule create_spec_file_hipp_native:
**inputs.subj_wildcards
),
surfname=["midthickness"],
space=["{space}", "unfold", "unfoldreg"],
space=["{space}", get_unfold_ref_name(wildcards)],
allow_missing=True,
),
cifti_metrics=lambda wildcards: inputs[config["modality"]].expand(
Expand Down Expand Up @@ -1879,7 +1875,7 @@ rule create_spec_file_dentate_native:
metric=get_gifti_metric_types(wildcards.label),
allow_missing=True,
),
surfs=expand(
surfs=lambda wildcards: expand(
bids(
root=root,
datatype="surf",
Expand All @@ -1890,7 +1886,7 @@ rule create_spec_file_dentate_native:
**inputs.subj_wildcards
),
surfname=["midthickness"],
space=["{space}", "unfold", "unfoldreg"],
space=["{space}", get_unfold_ref_name(wildcards)],
allow_missing=True,
),
cifti_metrics=lambda wildcards: inputs[config["modality"]].expand(
Expand Down Expand Up @@ -1925,6 +1921,72 @@ rule create_spec_file_dentate_native:
"{params.cmds}"


rule merge_lr_spec_file:
input:
spec_files=expand(
bids(
root=root,
datatype="surf",
suffix="surfaces.spec",
hemi="{hemi}",
space="{space}",
label="{autotop}",
**inputs.subj_wildcards
),
hemi=config["hemi"],
allow_missing=True,
),
params:
cmd=get_cmd_merge_spec,
output:
spec_file=bids(
root=root,
datatype="surf",
space="{space}",
suffix="surfaces.spec",
label="{autotop}",
**inputs.subj_wildcards
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"{params.cmd}"


rule merge_hipp_dentate_spec_file:
input:
spec_files=expand(
bids(
root=root,
datatype="surf",
suffix="surfaces.spec",
space="{space}",
label="{autotop}",
**inputs.subj_wildcards
),
autotop=config["autotop_labels"],
allow_missing=True,
),
params:
cmd=get_cmd_merge_spec,
output:
spec_file=bids(
root=root,
datatype="surf",
space="{space}",
suffix="surfaces.spec",
**inputs.subj_wildcards
),
container:
config["singularity"]["autotop"]
group:
"subj"
shell:
"{params.cmd}"


rule cp_native_surf_to_root:
input:
native=bids(
Expand Down
8 changes: 4 additions & 4 deletions hippunfold/workflow/rules/warps.smk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ rule create_unfold_ref:
orient=lambda wildcards: config["unfold_vol_ref"][wildcards.autotop]["orient"],
output:
nii=bids(
root=root,
root=work,
space="unfold",
label="{autotop}",
datatype="warps",
Expand All @@ -261,7 +261,7 @@ rule create_unfold_ref:
rule create_unfold_coord_map:
input:
nii=bids(
root=root,
root=work,
space="unfold",
label="{autotop}",
datatype="warps",
Expand Down Expand Up @@ -316,7 +316,7 @@ def get_laminar_coords(wildcards):
rule create_warps_hipp:
input:
unfold_ref_nii=bids(
root=root,
root=work,
space="unfold",
label="hipp",
datatype="warps",
Expand Down Expand Up @@ -409,7 +409,7 @@ rule create_warps_hipp:
rule create_warps_dentate:
input:
unfold_ref_nii=bids(
root=root,
root=work,
space="unfold",
label="dentate",
datatype="warps",
Expand Down

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