➖ removed space-template_desc-T1w_mask resource from outputs and replaced with space-template_desc-brain_mask for nodeblocks requesting it

Author: birajstha

CHANGELOG.md

@@ -44,6 +44,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `ABCD-HCP`
   - `fMRIPrep-LTS`
 - Typehinting support for Python < 3.10.
+- Resource `space-template_desc-T1w_mask`
+  - as output from FNIRT registration.
+  - as inputs from Nodeblocks requesting it and, replaced with `space-template_desc-brain_mask`.
+  - from outputs tsv.
+
 
 ## [1.8.7] - 2024-05-03
 

CPAC/func_preproc/func_preproc.py

@@ -1478,7 +1478,7 @@ def bold_mask_anatomical_based(wf, cfg, strat_pool, pipe_num, opt=None):
         "desc-preproc_bold",
         "T1w-template-funcreg",
         "space-template_desc-preproc_T1w",
-        "space-template_desc-T1w_mask",
+        "space-template_desc-brain_mask",
     ],
     outputs=[
         "space-template_res-bold_desc-brain_T1w",
@@ -1519,7 +1519,7 @@ def bold_mask_anatomical_resampled(wf, cfg, strat_pool, pipe_num, opt=None):
         "anatomical_registration"
     ]["registration"]["FSL-FNIRT"]["identity_matrix"]
 
-    node, out = strat_pool.get_data("space-template_desc-T1w_mask")
+    node, out = strat_pool.get_data("space-template_desc-brain_mask")
     wf.connect(node, out, anat_brain_mask_to_func_res, "in_file")
 
     wf.connect(

CPAC/registration/registration.py

@@ -2271,7 +2271,7 @@ def bold_to_T1template_xfm_connector(
     outputs={
         "space-template_desc-preproc_T1w": {"Template": "T1w-brain-template"},
         "space-template_desc-head_T1w": {"Template": "T1w-template"},
-        "space-template_desc-T1w_mask": {"Template": "T1w-template"},
+        "space-template_desc-brain_mask": {"Template": "T1w-template"},
         "space-template_desc-T1wT2w_biasfield": {"Template": "T1w-template"},
         "from-T1w_to-template_mode-image_desc-linear_xfm": {"Template": "T1w-template"},
         "from-template_to-T1w_mode-image_desc-linear_xfm": {"Template": "T1w-template"},
@@ -2896,7 +2896,6 @@ def register_ANTs_EPI_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
     outputs={
         "space-template_desc-preproc_T1w": {"Template": "T1w-template"},
         "space-template_desc-head_T1w": {"Template": "T1w-template"},
-        "space-template_desc-T1w_mask": {"Template": "T1w-template"},
         "from-T1w_to-template_mode-image_xfm": {"Template": "T1w-template"},
         "from-template_to-T1w_mode-image_xfm": {"Template": "T1w-template"},
     },
@@ -3116,10 +3115,6 @@ def overwrite_transform_anat_to_template(wf, cfg, strat_pool, pipe_num, opt=None
         outputs = {
             "space-template_desc-preproc_T1w": (apply_mask, "out_file"),
             "space-template_desc-head_T1w": (fsl_apply_warp_t1_to_template, "out_file"),
-            "space-template_desc-T1w_mask": (
-                fsl_apply_warp_t1_brain_mask_to_template,
-                "out_file",
-            ),
             "from-T1w_to-template_mode-image_xfm": (merge_xfms, "merged_file"),
             "from-template_to-T1w_mode-image_xfm": (merge_inv_xfms, "merged_file"),
         }
@@ -4419,7 +4414,7 @@ def warp_timeseries_to_T1template_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
             "from-bold_to-T1w_mode-image_desc-linear_warp",
             "T1w-template",
             "space-template_desc-head_T1w",
-            "space-template_desc-T1w_mask",
+            "space-template_desc-brain_mask",
             "space-template_desc-T1wT2w_biasfield",
         )
     ],
@@ -4480,7 +4475,7 @@ def warp_timeseries_to_T1template_dcan_nhp(wf, cfg, strat_pool, pipe_num, opt=No
         "anatomical_registration"
     ]["registration"]["FSL-FNIRT"]["identity_matrix"]
 
-    node, out = strat_pool.get_data("space-template_desc-T1w_mask")
+    node, out = strat_pool.get_data("space-template_desc-brain_mask")
     wf.connect(node, out, applywarp_anat_mask_res, "in_file")
     wf.connect(applywarp_anat_res, "out_file", applywarp_anat_mask_res, "ref_file")
 

CPAC/resources/cpac_outputs.tsv

@@ -166,7 +166,6 @@ desc-restore-brain_T1w	T1w	T1w	anat	NIfTI
 space-template_desc-brain_T1w	T1w	template	anat	NIfTI				Yes	
 space-template_desc-preproc_T1w	T1w	template	anat	NIfTI					
 space-template_desc-head_T1w	T1w	template	anat	NIfTI					
-space-template_desc-T1w_mask	mask	template	anat	NIfTI					
 space-template_desc-Mean_timeseries	timeseries		func	1D					
 desc-MeanSCA_timeseries	timeseries		func	1D					
 desc-SpatReg_timeseries	timeseries		func	1D					

CPAC/surface/surf_preproc.py

@@ -928,7 +928,7 @@ def run_surface(
             [
                 "space-template_desc-head_T1w",
                 "space-template_desc-brain_T1w",
-                "space-template_desc-T1w_mask",
+                "space-template_desc-brain_mask",
             ],
             [
                 "from-T1w_to-template_mode-image_xfm",
@@ -1202,7 +1202,7 @@ def surface_postproc(wf, cfg, strat_pool, pipe_num, opt=None):
     space_temp = [
         "space-template_desc-head_T1w",
         "space-template_desc-brain_T1w",
-        "space-template_desc-T1w_mask",
+        "space-template_desc-brain_mask",
     ]
     atlas_xfm = [
         "from-T1w_to-template_mode-image_xfm",