remove corobl resample, add crop, --resample-manualseg

hippunfold/config/snakebids.yml

@@ -171,6 +171,11 @@ parse_args:
     help: 'Sets the bounding box size for the crop native (e.g. cropT1w space). Make this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off. This must be in voxels (vox) not millimeters (mm). (default: %(default)s)'
     default: '256x256x256vox'
 
+  --resample_manualseg:
+    help: 'Resample the manual segmentation (for --modality manualseg), keeping the bounding box the same, but changing the number of voxels in the image. This can be specified as voxels ("300x300x300"), or a percentage ("20%%") or percentage in each direction ("20x20x40%%"). Note: the segmentation will always be subsequently cropped around the segmentation, with a padding of 5 voxels.  (default: %(default)s)'
+    default: null
+
+
   --atlas:
     choices:
       - 'multihist7'
@@ -688,3 +693,4 @@ root: results
 workdir: null
 use_template_seg: False
 template_seg_smoothing_factor: 2
+resample_manualseg: null

hippunfold/workflow/rules/preproc_manualseg.smk

@@ -1,54 +1,24 @@
-config["resample_inplace"] = "20%"
 
-if config["resample_inplace"] is not None:
-
-    rule import_manualseg:
-        input:
-            in_img=partial(get_single_bids_input, component="manualseg"),
-        params:
-            resample=config["resample_inplace"],
-        output:
-            nii=bids(
-                root=work,
-                datatype="anat",
-                **inputs.subj_wildcards,
-                suffix="dseg.nii.gz",
-                space="corobl",
-                hemi="{hemi,L|R}",
-            ),
-        group:
-            "subj"
-        shell:
-            "c3d {input} -int 0 -resample {params.resample} -o {output}"
-
-else:
-
-    rule import_manualseg_to_corobl:
-        input:
-            in_img=partial(get_single_bids_input, component="manualseg"),
-            template_dir=Path(download_dir) / "template" / config["template"],
-        params:
-            std_to_cor=lambda wildcards, input: Path(input.template_dir)
-            / config["template_files"][config["template"]]["xfm_corobl"].format(
-                **wildcards
-            ),
-            ref=lambda wildcards, input: Path(input.template_dir)
-            / config["template_files"][config["template"]]["crop_ref"].format(
-                **wildcards
-            ),
-        output:
-            nii=bids(
-                root=work,
-                datatype="anat",
-                **inputs.subj_wildcards,
-                suffix="dseg.nii.gz",
-                space="corobl",
-                hemi="{hemi,L|R}",
-            ),
-        container:
-            config["singularity"]["autotop"]
-        group:
-            "subj"
-        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 import_manualseg_with_resample:
+    input:
+        in_img=partial(get_single_bids_input, component="manualseg"),
+    params:
+        resample_cmd=""
+        if config["resample_manualseg"] == None
+        else "-resample {res}".format(res=config["resample_manualseg"]),
+        crop_cmd="-trim 5vox",  #leave 5 voxel padding
+    output:
+        nii=bids(
+            root=work,
+            datatype="anat",
+            **inputs.subj_wildcards,
+            suffix="dseg.nii.gz",
+            space="corobl",
+            hemi="{hemi,L|R}",
+        ),
+    container:
+        config["singularity"]["autotop"]
+    group:
+        "subj"
+    shell:
+        "c3d {input} -int 0 {params.resample_cmd} {params.crop_cmd} -o {output}"