petpal 0.5.10__py3-none-any.whl → 0.6.0__py3-none-any.whl

petpal/cli/cli_preproc.py

@@ -83,7 +83,12 @@ Examples:
    .. code-block:: bash
 
        petpal-preproc warp-pet-atlas -i /path/to/input_img.nii.gz -o petpal_reg-atlas.nii.gz --anatomical /path/to/anat.nii.gz --reference-atlas /path/to/atlas.nii.gz
- 
+
+    * Crop segmentation to PET FOV:
+
+    .. code-block:: bash
+
+        petpal-preproc seg-crop -i /path/to/input_img.nii.gz -o petpal_cropped_seg.nii.gz --segmentation /path/to/segmentation.nii.gz
 
 See Also:
     * :mod:`~petpal.preproc.image_operations_4d` - module used for operations on 4D images.
@@ -99,7 +104,8 @@ from ..preproc import (image_operations_4d,
                        motion_corr,
                        register,
                        regional_tac_extraction,
-                       standard_uptake_value)
+                       standard_uptake_value,
+                       segmentation_tools)
 
 
 _PREPROC_EXAMPLES_ = r"""
@@ -126,6 +132,10 @@ Examples:
     petpal-preproc warp-pet-atlas -i /path/to/input_img.nii.gz -o petpal_reg-atlas.nii.gz --anatomical /path/to/anat.nii.gz --reference-atlas /path/to/atlas.nii.gz
   - SUV:
     petpal-preproc suv -i /path/to/input_img.nii.gz -o petpal_suv.nii.gz --weight 75 --dose 250 --start-time 1200 --end-time 3600
+  - Crop segmentation image to PET FOV:
+    petpal-preproc seg-crop -i /path/to/input_img.nii.gz -o petpal_cropped_seg.nii.gz --segmentation /path/to/segmentation.nii.gz
+  - Add eroded white matter region to segmentation image:
+    petpal-preproc eroded-wm -i /path/to/input_segmentation.nii.gz -o petpal_seg_with_eroded_wm.nii.gz
 """
 
 
@@ -357,6 +367,19 @@ def _generate_args() -> argparse.ArgumentParser:
                             required=True,
                             help='End time for SUV calculation in seconds from scan start',
                             type=float)
+
+    parser_seg_crop = subparsers.add_parser('seg-crop',help='Crop segmentation image to PET FOV')
+    _add_common_args(parser_seg_crop)
+    parser_seg_crop.add_argument('-s',
+                                 '--segmentation',
+                                 required=True,
+                                 help='Path to segmentation image',
+                                 type=str)
+
+    parser_eroded_wm = subparsers.add_parser('eroded-wm',
+                                             help='Add eroded white matter region to segmentation image')
+    _add_common_args(parser_eroded_wm)
+
     return parser
 
 
@@ -454,6 +477,15 @@ def main():
                                       end_time=args.end_time,
                                       weight=args.weight,
                                       dose=args.dose)
+        case 'seg_crop':
+            input_img = ants.image_read(filename=args.input_img)
+            seg_img = ants.image_read(filename=args.segmentation)
+            seg_cropped = segmentation_tools.seg_crop_to_pet_fov(pet_img=input_img,
+                                                                 segmentation_img=seg_img)
+            ants.image_write(seg_cropped,args.out_img)
+        case 'eroded_wm':
+            segmentation_tools.eroded_wm_segmentation(input_segmentation_path=args.input_img,
+                                                      out_segmentation_path=args.out_img)
 
 if __name__ == "__main__":
     main()

petpal/preproc/segmentation_tools.py

@@ -84,7 +84,9 @@ def segmentations_merge(segmentation_primary: np.ndarray,
             regions added.
     """
     for region in regions:
-        region_mask = (segmentation_secondary > region - 0.1) & (segmentation_secondary < region + 0.1)
+        condition_above = segmentation_secondary > region - 0.1
+        condition_below = segmentation_secondary < region + 0.1
+        region_mask = condition_above & condition_below
         segmentation_primary[region_mask] = region
     return segmentation_primary
 
@@ -229,8 +231,9 @@ def resample_segmentation(input_image_path: str,
     seg_image = nibabel.load(segmentation_image_path)
     pet_series = pet_image.get_fdata()
     image_first_frame = pet_series[:, :, :, 0]
+    to_vox_map_tuple = (image_first_frame.shape, pet_image.affine)
     seg_resampled = processing.resample_from_to(from_img=seg_image,
-                                                to_vox_map=(image_first_frame.shape, pet_image.affine),
+                                                to_vox_map=to_vox_map_tuple,
                                                 order=0)
     nibabel.save(seg_resampled, out_seg_path)
     if verbose:
@@ -238,23 +241,30 @@ def resample_segmentation(input_image_path: str,
 
 
 def vat_wm_ref_region(input_segmentation_path: str,
-                      out_segmentation_path: str):
+                      out_segmentation_path: str | None) -> ants.ANTsImage:
     """
     Generates the cortical white matter reference region described in O'Donnell
-    JL et al. (2024) PET Quantification of [18F]VAT in Human Brain and Its 
+    JL et al. (2024).
+     
+    Reference: O'Donnell JL et al. (2024). PET Quantification of [18F]VAT in Human Brain and Its 
     Test-Retest Reproducibility and Age Dependence. J Nucl Med. 2024 Jun 
     3;65(6):956-961. doi: 10.2967/jnumed.123.266860. PMID: 38604762; PMCID:
-    PMC11149597. Requires FreeSurfer segmentation with original label mappings.
+    PMC11149597.
+    
+    Requires FreeSurfer segmentation with original label mappings. 
 
     Args:
         input_segmentation_path (str): Path to segmentation on which white
             matter reference region is computed.
         out_segmentation_path (str): Path to which white matter reference
             region mask image is saved.
+
+    Returns:
+        wm_erode (ants.ANTsImage): Eroded white matter reference region mask image.
     """
     wm_regions = [2,41,251,252,253,254,255,77,3000,3001,3002,3003,3004,3005,
                   3006,3007,3008,3009,3010,3011,3012,3013,3014,3015,3016,3017,
-                  3018,3019,3020,3021,3022,3023,3024,3025,3026,3027,3018,3029,
+                  3018,3019,3020,3021,3022,3023,3024,3025,3026,3027,3028,3029,
                   3030,3031,3032,3033,3034,3035,4000,4001,4002,4003,4004,4005,
                   4006,4007,4008,4009,4010,4011,4012,4013,4014,4015,4016,4017,
                   4018,4019,4020,4021,4022,4023,4024,4025,4026,4027,4028,4029,
@@ -277,7 +287,45 @@ def vat_wm_ref_region(input_segmentation_path: str,
     wm_csf_eroded = ants.threshold_image(image=wm_csf_blurred, low_thresh=0.95, binary=True)
     wm_erode = ants.mask_image(image=wm_merged, mask=wm_csf_eroded)
 
-    ants.image_write(image=wm_erode, filename=out_segmentation_path)
+    if out_segmentation_path is not None:
+        ants.image_write(image=wm_erode, filename=out_segmentation_path)
+
+    return wm_erode
+
+
+def eroded_wm_segmentation(input_segmentation_path: str,
+                           out_segmentation_path: str | None,
+                           eroded_wm_region_mapping: int = 1) -> ants.ANTsImage:
+    """
+    Generates eroded white matter region on a segmentation image and merges it into the image,
+    saving result as a new segmentation image.
+
+    Requires FreeSurfer segmentation with original label mappings.
+    
+    Args:
+        input_segmentation_path (str): Path to input freesurfer segmentation, such as aparc+aseg or
+            wmparc.
+        out_segmentation_path (str): Path to output segmentation image with replaced values in
+            eroded whited matter region.
+        eroded_wm_region_mapping (int): Segmentation mapping for the eroded white matter region in
+            the output image. Default "1".
+
+    Returns:
+        seg_img (ants.ANTsImage): Input segmentation image with values in eroded white matter
+            replaced with `eroded_wm_region_mapping`.
+
+    See also:
+        :meth:`~petpal.preproc.segmentation_tools.vat_wm_ref_region` - function that generates the
+            eroded white matter region.
+    """
+    wm_erode = vat_wm_ref_region(input_segmentation_path=input_segmentation_path,
+                                 out_segmentation_path=None)
+    seg_img = ants.image_read(input_segmentation_path)
+    seg_img[wm_erode==1] = int(eroded_wm_region_mapping)
+    if out_segmentation_path is not None:
+        ants.image_write(image=seg_img, filename=out_segmentation_path)
+
+    return seg_img
 
 
 def vat_wm_region_merge(wmparc_segmentation_path: str,
@@ -500,7 +548,8 @@ def calc_vesselness_mask_from_quantiled_vesselness(input_image: ants.core.ANTsIm
                                                    morph_dil_radius: int = 0,
                                                    z_crop: int = 3) -> ants.core.ANTsImage:
     """
-    Generates a binary vesselness mask from a given vesselness image using quantile-based thresholding.
+    Generates a binary vesselness mask from a given vesselness image using quantile-based
+    thresholding.
 
     This function creates a binary mask by thresholding a vesselness image at a specified
     quantile of non-zero voxel values. Additionally, it allows for optional z-axis cropping

{petpal-0.5.10.dist-info → petpal-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: petpal
-Version: 0.5.10
+Version: 0.6.0
 Summary: PET-PAL (Positron Emission Tomography Processing and Analysis Library)
 Project-URL: Repository, https://github.com/PETPAL-WUSM/PETPAL.git
 Author-email: Noah Goldman <noahg@wustl.edu>, Bradley Judge <bjudge@wustl.edu>, Furqan Dar <dar@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>

{petpal-0.5.10.dist-info → petpal-0.6.0.dist-info}/RECORD

@@ -6,7 +6,7 @@ petpal/cli/cli_idif.py,sha256=6lh_kJHcGjlHDXZOvbiuHrNqpk5FovVV5_j7_dPHTHU,5145
 petpal/cli/cli_parametric_images.py,sha256=JBFb8QlxZoGOzqvCJPFuZ7czzGWntJP5ZcfeM5-QF4Y,7385
 petpal/cli/cli_pib_processing.py,sha256=ye_yw0ZQ4cSrMNemGR7cU9v6epD7Wbq1xaNAJwLzV_8,6889
 petpal/cli/cli_plot_tacs.py,sha256=XycaYQQl9Jp5jqDp3QXOlVT2sXHYYpYSraEArxsfJec,6479
-petpal/cli/cli_preproc.py,sha256=y5YvRliXC3zNY8oBJgTkzwPH9YNwWnEUWgiltUAv7AU,21850
+petpal/cli/cli_preproc.py,sha256=Wy0Y_2hTXg_Xyg2F7xOA93B4X4wzKX6QJDkB5mSikOI,23607
 petpal/cli/cli_pvc.py,sha256=DC0JZ6p1pkc5BDgQ006bi9y0Mz32ENrjUaOtSvFobP4,3967
 petpal/cli/cli_reference_tissue_models.py,sha256=18BlKN4rMehyFbdq_yr88oztqR99_gBtWKImhwf7CQY,13283
 petpal/cli/cli_stats.py,sha256=Mqbzc9yYo9SVAfxzaYbAbk7EheW472l1PY_ptlD1DOI,2050
@@ -44,7 +44,7 @@ petpal/preproc/motion_target.py,sha256=_OJp3NoYcyD3Ke3wl2KbfOhbJ6dp6ZduR9LLz0rIa
 petpal/preproc/partial_volume_corrections.py,sha256=J06j_Y_lhj3b3b9M5FbB2r2EPWQvoymG3GRUffSlYdE,6799
 petpal/preproc/regional_tac_extraction.py,sha256=ZXo2u-EAUg5wZj7GGYLMEaOAfLv8OCOR-Gd0xvih6Y4,22358
 petpal/preproc/register.py,sha256=NKg8mt_XMGa5HBdxYZh3sMu_KMJ0W41VHlX4Zl8wlyE,14171
-petpal/preproc/segmentation_tools.py,sha256=Xi1ZnBs3sp23MHWPPOLjuXi6qp4-igwIPXFJ4B_Yzsk,27186
+petpal/preproc/segmentation_tools.py,sha256=CDD0NWV23rkNB56HjZGLsO4HbV61O57KsNzQsR4d06g,29106
 petpal/preproc/standard_uptake_value.py,sha256=YJIt0fl3fwMLl0tRYHpPPprMTaN4Q5JjQ5dx_CQX1nI,7494
 petpal/preproc/symmetric_geometric_transfer_matrix.py,sha256=Sr5qMTiNC76ZRKiGG5So7fceV_Lr0ql7UybO_kJgmNo,20360
 petpal/utils/__init__.py,sha256=PlxBIKUtNvtSFnNZqz8myszOysaYzS8nSILMK4haVGg,412
@@ -65,8 +65,8 @@ petpal/visualizations/graphical_plots.py,sha256=ZCKUeLX2TAQscuHjA4bzlFm1bACHIyCw
 petpal/visualizations/image_visualization.py,sha256=Ob6TD4Q0pIrxi0m9SznK1TRWbX1Ea9Pt4wNMdRrTfTs,9124
 petpal/visualizations/qc_plots.py,sha256=iaCPe-LWWyM3OZzDPZodHZhP-z5fRdpUgaH7QS9VxPM,1243
 petpal/visualizations/tac_plots.py,sha256=zSGdptL-EnqhfDViAX8LFunln5a1b-NJ5ft7ZDcxQ38,15116
-petpal-0.5.10.dist-info/METADATA,sha256=QadOtBFu8TbKNi-WDticmziZXkREKywO0pP4F-AxAcI,2618
-petpal-0.5.10.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-petpal-0.5.10.dist-info/entry_points.txt,sha256=0SZmyXqBxKzQg2eerDA16n2BdUEXyixEm0_AUo2dFns,653
-petpal-0.5.10.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-petpal-0.5.10.dist-info/RECORD,,
+petpal-0.6.0.dist-info/METADATA,sha256=L5uinIwYmIUU0Ie_1wiLf-9TDeUeJrq6cHUuVXKSIq0,2617
+petpal-0.6.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+petpal-0.6.0.dist-info/entry_points.txt,sha256=0SZmyXqBxKzQg2eerDA16n2BdUEXyixEm0_AUo2dFns,653
+petpal-0.6.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+petpal-0.6.0.dist-info/RECORD,,