manualseg resampling in-place without transformation (#346)

* add option to resample in-place, without transforming to template corobl or assuming any kind of registration already
* add cropping tight (with 5 vox pad) to dseg

Author: akhanf

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

@@ -1,15 +1,12 @@
 
-rule import_manualseg_to_corobl:
+rule import_manualseg_with_resample:
     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),
+        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,
@@ -24,5 +21,4 @@ rule import_manualseg_to_corobl:
     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}"
+        "c3d {input} -int 0 {params.resample_cmd} {params.crop_cmd} -o {output}"