initial atempt, not yet wetrun tested

khanlab · Dec 17, 2024 · 3c93675 · 3c93675
1 parent f642963
commit 3c93675
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Showing 8 changed files with 284 additions and 412 deletions.
diff --git a/hippunfold/workflow/rules/gifti.smk b/hippunfold/workflow/rules/gifti.smk
@@ -1,5 +1,5 @@
 # lookup tables for structure:
-hemi_to_structure = {"L": "CORTEX_LEFT", "Lflip": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
+hemi_to_structure = {"L": "CORTEX_LEFT", "R": "CORTEX_RIGHT"}
 surf_to_secondary_type = {
     "midthickness": "MIDTHICKNESS",
     "inner": "PIAL",

diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
@@ -133,15 +133,15 @@ rule run_inference:
             suffix="dseg.nii.gz",
             desc="nnunet",
             space="corobl",
-            hemi="{hemi,Lflip|R}"
+            hemi="{hemi}"
         ),
     log:
         bids(
             root="logs",
             **inputs.subj_wildcards,
             suffix="nnunet.txt",
             space="corobl",
-            hemi="{hemi,Lflip|R}"
+            hemi="{hemi}"
         ),
     shadow:
         "minimal"
@@ -171,47 +171,6 @@ rule run_inference:
         "cp {params.temp_lbl} {output.nnunet_seg}"
 
 
-rule unflip_nnunet_nii:
-    """Unflip the Lflip nnunet seg"""
-    input:
-        nnunet_seg=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            desc="nnunet",
-            space="corobl",
-            hemi="{hemi}flip"
-        ),
-        unflip_ref=(
-            bids(
-                root=work,
-                datatype="anat",
-                **inputs.subj_wildcards,
-                suffix="{modality}.nii.gz".format(modality=config["modality"]),
-                space="corobl",
-                desc="preproc",
-                hemi="{hemi}",
-            ),
-        ),
-    output:
-        nnunet_seg=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            desc="nnunet",
-            space="corobl",
-            hemi="{hemi,L}"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input.nnunet_seg} -flip x -popas FLIPPED "
-        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nnunet_seg} "
-
 
 def get_f3d_ref(wildcards, input):
     if config["modality"] == "T2w":

diff --git a/hippunfold/workflow/rules/preproc_hippb500.smk b/hippunfold/workflow/rules/preproc_hippb500.smk
@@ -35,32 +35,6 @@ rule resample_hippdwi_to_template:
         " -trim 0vox -o {output}"
 
 
-rule lr_flip_b500:
-    input:
-        nii=bids(
-            root=work,
-            datatype="dwi",
-            **inputs.subj_wildcards,
-            suffix="b500.nii.gz",
-            space="corobl",
-            hemi="{hemi}"
-        ),
-    output:
-        nii=bids(
-            root=work,
-            datatype="dwi",
-            **inputs.subj_wildcards,
-            suffix="b500.nii.gz",
-            space="corobl",
-            hemi="{hemi,L}flip"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input} -flip x -o  {output}"
-
 
 rule cp_b500_to_anat_dir:
     input:

diff --git a/hippunfold/workflow/rules/preproc_manualseg.smk b/hippunfold/workflow/rules/preproc_manualseg.smk
@@ -25,30 +25,3 @@ rule import_manualseg_to_corobl:
     shell:
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
         "antsApplyTransforms -d 3 --interpolation MultiLabel -i {input.in_img} -o {output.nii} -r {params.ref} -t {params.std_to_cor}"
-
-
-rule lr_flip_seg:
-    input:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            space="corobl",
-            hemi="{hemi}"
-        ),
-    output:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="dseg.nii.gz",
-            space="corobl",
-            hemi="{hemi,L}flip"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input} -flip x -o  {output}"
diff --git a/hippunfold/workflow/rules/preproc_t1.smk b/hippunfold/workflow/rules/preproc_t1.smk
@@ -103,31 +103,3 @@ rule warp_t1_to_corobl_crop:
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
         "antsApplyTransforms -d 3 --interpolation Linear -i {input.t1} -o {output.t1} -r {params.ref}  -t {input.xfm}"
 
-
-rule lr_flip_t1:
-    input:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="T1w.nii.gz",
-            space="corobl",
-            desc="{desc}",
-            hemi="{hemi}"
-        ),
-    output:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="T1w.nii.gz",
-            space="corobl",
-            desc="{desc}",
-            hemi="{hemi,L}flip"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input} -flip x -o  {output}"
diff --git a/hippunfold/workflow/rules/preproc_t2.smk b/hippunfold/workflow/rules/preproc_t2.smk
@@ -413,31 +413,3 @@ rule warp_t2_to_corobl_crop:
         "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
         "antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output.nii} -r {params.ref}  -t {input.xfm}"
 
-
-rule lr_flip_t2:
-    input:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="T2w.nii.gz",
-            space="corobl",
-            desc="{desc}",
-            hemi="{hemi}"
-        ),
-    output:
-        nii=bids(
-            root=work,
-            datatype="anat",
-            **inputs.subj_wildcards,
-            suffix="T2w.nii.gz",
-            space="corobl",
-            desc="{desc}",
-            hemi="{hemi,L}flip"
-        ),
-    container:
-        config["singularity"]["autotop"]
-    group:
-        "subj"
-    shell:
-        "c3d {input} -flip x -o  {output}"