update from dbsc -> scattr

khanlab · Feb 12, 2023 · 67bcd32 · 67bcd32
1 parent fc1deb5
commit 67bcd32
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diff --git a/Dockerfile b/Dockerfile
@@ -18,5 +18,5 @@ RUN mkdir -p /opt \
 
 # Stage: runtime
 FROM build AS runtime
-COPY ./dbsc /opt/dbsc
-# ENTRYPOINT ["/opt/dbsc/run.py"]
+COPY ./scattr /opt/scattr
+# ENTRYPOINT ["/opt/scattr/run.py"]
diff --git a/README.md b/README.md
@@ -1,8 +1,6 @@
-## Deep Brain Structural Connectivity (DBSC)
+## Structural Connectivity Applied To Targetted Regions (SCATTR)
 
-**Development in-progress** (conversion from shell scripts)
-
-DBSC is a BIDS App that performs tractography to identify
+SCATTR is a BIDS App that performs tractography to identify
 connections between subcortical structures (i.e. map the subcortical
 connectome), making use of existing neuroimaging tools like `prepdwi`,
 `Freesurfer`, and `Mrtrix3`.
@@ -11,7 +9,7 @@ This workflow was used to process the data for the analysis from
 [`hcp_subcortical_repo`](https://github.com/kaitj/hcp_subcortical_repro).
 
 ### Contributing
-Clone the git repository. DBSC dependencies are managed with Poetry
+Clone the git repository. SCATTR dependencies are managed with Poetry
 (version 1.2.x), which you'll need installed on your machine.
 You can find instructions on the Poetry
 [website](https://python-poetry.org/docs/).
@@ -23,7 +21,7 @@ poetry install
 poetry run poe setup
 ```
 
-DBSC uses poethepoet as a task runner.
+SCATTR uses poethepoet as a task runner.
 You can see what commands are available by running:
 
 ```
@@ -33,7 +31,7 @@ poetry run poe
 If you wish, you can also run poe [command] directly by installing poethepoet
 on your system. Follow the install instructions at the link above.
 
-DBSC uses pre-commit hooks (installed via the poe setup command above) to lint
+SCATTR uses pre-commit hooks (installed via the poe setup command above) to lint
 and format code (we use black, isort, flake8). By default, these hooks are
 run on every commit.
 

diff --git a/dbsc/pipeline_description.json b/dbsc/pipeline_description.json
diff --git a/dbsc/resources/zona_bb_subcortex/transforms/README.md b/dbsc/resources/zona_bb_subcortex/transforms/README.md
diff --git a/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w0GenericAffine.mat b/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w0GenericAffine.mat
diff --git a/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w1InverseWarp.nii.gz b/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w1InverseWarp.nii.gz
diff --git a/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w1Warp.nii.gz b/dbsc/resources/zona_bb_subcortex/transforms/mni2009b-to-mni152-T1w1Warp.nii.gz
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
-name = "Deep Brain Structural Connectivity"
+name = "scattr"
 version = "0.1.0-pre.1"
-description = "Snakebids app for mapping the subcortical connectome"
+description = "Snakebids app for structural connectivity between targetted regions"
 authors = [
     "Jason Kai <tkai@uwo.ca>",
     "Tristan Kuehn",
@@ -38,13 +38,13 @@ build-backend = "poetry.core.masonry.api"
 setup = "pre-commit install"
 yamlfix = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix {} \\;" }
 yamlfix-check = { shell = "find . -type f \\( -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* ! -iname snakebids* \\) -exec yamlfix --check {} \\;" }
-isort = "isort dbsc"
-isort-check = "isort -c dbsc"
-black = "black dbsc"
-black-check = "black --check dbsc"
-flake8 = "flake8 dbsc"
-snakefmt = "snakefmt dbsc"
-snakefmt-check = "snakefmt --check dbsc"
+isort = "isort scattr"
+isort-check = "isort -c scattr"
+black = "black scattr"
+black-check = "black --check scattr"
+flake8 = "flake8 scattr"
+snakefmt = "snakefmt scattr"
+snakefmt-check = "snakefmt --check scattr"
 quality = ["yamlfix", "isort", "black", "flake8", "snakefmt"]
 quality-check = [
     "yamlfix-check",
@@ -53,10 +53,10 @@ quality-check = [
     "flake8",
     "snakefmt-check",
 ]
-test_base = { shell = "python ./dbsc/run.py ./test/data/bids ./test/data/derivatives/ participant -np --force-output" }
-test_freesurfer = { shell = "python ./dbsc/run.py ./test/data/bids test/data/derivatives/ participant --freesurfer_dir ./test/data/derivatives/freesurfer -np --force-output" }
-test_responsemean = { shell = "python ./dbsc/run.py ./test/data/bids test/data/derivatives/ participant --responsemean_dir ./test/data/derivatives/mrtrix/avg -np --force-output" }
-test_dwi = { shell = "python ./dbsc/run.py ./test/data/bids_nodwi test/data/derivatives/ participant --dwi_dir ./test/data/derivatives/prepdwi -np --force-output" }
+test_base = { shell = "python ./scattr/run.py ./test/data/bids ./test/data/derivatives/ participant -np --force-output" }
+test_freesurfer = { shell = "python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant --freesurfer_dir ./test/data/derivatives/freesurfer -np --force-output" }
+test_responsemean = { shell = "python ./scattr/run.py ./test/data/bids test/data/derivatives/ participant --responsemean_dir ./test/data/derivatives/mrtrix/avg -np --force-output" }
+test_dwi = { shell = "python ./scattr/run.py ./test/data/bids_nodwi test/data/derivatives/ participant --dwi_dir ./test/data/derivatives/prepdwi -np --force-output" }
 test = ["test_base", "test_freesurfer", "test_responsemean", "test_dwi"]
 
 [tool.isort]

diff --git a/dbsc/config/snakebids.yml → scattr/config/snakebids.yml b/dbsc/config/snakebids.yml → scattr/config/snakebids.yml
@@ -181,11 +181,11 @@ freesurfer:
 # Containers
 # NOTE: Update from latest to use specific tags
 singularity:
-  freesurfer: /project/6050199/akhanf/singularity/bids-apps/pwighton_freesurfer_7.1.0.sif # "docker://pwighton/freesurfer:7.2.0"
-  neuroglia-core: /project/6050199/akhanf/singularity/bids-apps/khanlab_neuroglia-core_latest.sif # "docker://khanlab/neuroglia-core:latest"
-  ants: /project/6050199/akhanf/singularity/kaczmarj_ants_2.3.4.sif # "docker://kaczmarj/ants:2.3.4"
-  mrtrix: /project/6050199/tkai/singularity/mrtrix3_3.0.3_parallel.sif # "docker://brainlife/mrtrix3:3.0.3"
-  labelmerge: /project/6050199/tkai/singularity/labelmerge_v0.1.0.sif # "docker://kaitj/labelmerge:v0.1.0"
-  dbsc: /project/6050199/tkai/singularity/dbsc_v0.1.0.sif # "docker:kaitj/dbsc:v0.1.0"
-
-fs_license: /project/6050199/akhanf/opt/freesurfer/.license # /path/to/fs/license
+  freesurfer: "docker://pwighton/freesurfer:7.2.0"
+  neuroglia-core: "docker://khanlab/neuroglia-core:latest"
+  ants: "docker://kaczmarj/ants:2.3.4"
+  mrtrix: "docker://brainlife/mrtrix3:3.0.3"
+  labelmerge: "docker://kaitj/labelmerge:v0.1.0"
+  scattr: "docker:kaitj/scattr:v0.1.0"
+
+fs_license: /path/to/fs/license
diff --git a/scattr/pipeline_description.json b/scattr/pipeline_description.json
@@ -0,0 +1,14 @@
+{
+    "Name": "Structural Connectivity Applied To Targetted Regions (SCATTR)",
+    "BIDSVersion": "1.4.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        { 
+            "Name": "Structural Connectivity Applied To Targetted Regions (SCATTR)",
+            "Version": "0.1.0",
+            "CodeURL": "https://github.com/khanlab/scattr",
+            "Author": "Jason Kai",
+            "AuthorEmail": "tkai@uwo.ca"
+        }
+    ]
+}
diff --git a/dbsc/resources/example_scripts/README.md → scattr/resources/example_scripts/README.md b/dbsc/resources/example_scripts/README.md → scattr/resources/example_scripts/README.md
diff --git a/...example_scripts/freesurfer/2_thalamusparc → ...example_scripts/freesurfer/2_thalamusparc b/...example_scripts/freesurfer/2_thalamusparc → ...example_scripts/freesurfer/2_thalamusparc
diff --git a/...e_scripts/mrtpipelines/0_run-mrtpipelines → ...e_scripts/mrtpipelines/0_run-mrtpipelines b/...e_scripts/mrtpipelines/0_run-mrtpipelines → ...e_scripts/mrtpipelines/0_run-mrtpipelines
diff --git a/...ts/mrtpipelines/2_run-mrtpipelines-native → ...ts/mrtpipelines/2_run-mrtpipelines-native b/...ts/mrtpipelines/2_run-mrtpipelines-native → ...ts/mrtpipelines/2_run-mrtpipelines-native
diff --git a/...elines/3_run-mrtpipelines-subcorticalconn → ...elines/3_run-mrtpipelines-subcorticalconn b/...elines/3_run-mrtpipelines-subcorticalconn → ...elines/3_run-mrtpipelines-subcorticalconn
diff --git a/...rtpipelines/4_run-mrtpipelines-maskedconn → ...rtpipelines/4_run-mrtpipelines-maskedconn b/...rtpipelines/4_run-mrtpipelines-maskedconn → ...rtpipelines/4_run-mrtpipelines-maskedconn
diff --git a/...cripts/mrtpipelines/4b_subconn_maskedeval → ...cripts/mrtpipelines/4b_subconn_maskedeval b/...cripts/mrtpipelines/4b_subconn_maskedeval → ...cripts/mrtpipelines/4b_subconn_maskedeval
diff --git a/...ple_scripts/mrtpipelines/5_run-cleanTract → ...ple_scripts/mrtpipelines/5_run-cleanTract b/...ple_scripts/mrtpipelines/5_run-cleanTract → ...ple_scripts/mrtpipelines/5_run-cleanTract
diff --git a/...ipelines/6_run-mrtpipelines-combineMasked → ...ipelines/6_run-mrtpipelines-combineMasked b/...ipelines/6_run-mrtpipelines-combineMasked → ...ipelines/6_run-mrtpipelines-combineMasked
diff --git a/...s/example_scripts/mrtpipelines/extractCST → ...s/example_scripts/mrtpipelines/extractCST b/...s/example_scripts/mrtpipelines/extractCST → ...s/example_scripts/mrtpipelines/extractCST
diff --git a/...s/example_scripts/mrtpipelines/getSubconn → ...s/example_scripts/mrtpipelines/getSubconn b/...s/example_scripts/mrtpipelines/getSubconn → ...s/example_scripts/mrtpipelines/getSubconn
diff --git a/...urces/example_scripts/mrtpipelines/getTDI → ...urces/example_scripts/mrtpipelines/getTDI b/...urces/example_scripts/mrtpipelines/getTDI → ...urces/example_scripts/mrtpipelines/getTDI
diff --git a/...cripts/zona_bb_subcortex/addFSThalamus.sh → ...cripts/zona_bb_subcortex/addFSThalamus.sh b/...cripts/zona_bb_subcortex/addFSThalamus.sh → ...cripts/zona_bb_subcortex/addFSThalamus.sh
diff --git a/...pts/zona_bb_subcortex/applyXfrm_ZonaBB.sh → ...pts/zona_bb_subcortex/applyXfrm_ZonaBB.sh b/...pts/zona_bb_subcortex/applyXfrm_ZonaBB.sh → ...pts/zona_bb_subcortex/applyXfrm_ZonaBB.sh
diff --git a/..._scripts/zona_bb_subcortex/convexHull_roi → ..._scripts/zona_bb_subcortex/convexHull_roi b/..._scripts/zona_bb_subcortex/convexHull_roi → ..._scripts/zona_bb_subcortex/convexHull_roi
diff --git a/...s/freesurfer/desc-FreesurferThal_dseg.tsv → ...s/freesurfer/desc-FreesurferThal_dseg.tsv b/...s/freesurfer/desc-FreesurferThal_dseg.tsv → ...s/freesurfer/desc-FreesurferThal_dseg.tsv
diff --git a/...in2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz → ...in2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz b/...in2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz → ...in2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz
diff --git a/...NLin2009bAsym_hemi-L_desc-fct_mask.nii.gz → ...NLin2009bAsym_hemi-L_desc-fct_mask.nii.gz b/...NLin2009bAsym_hemi-L_desc-fct_mask.nii.gz → ...NLin2009bAsym_hemi-L_desc-fct_mask.nii.gz
diff --git a/...2NLin2009bAsym_hemi-L_desc-fl_mask.nii.gz → ...2NLin2009bAsym_hemi-L_desc-fl_mask.nii.gz b/...2NLin2009bAsym_hemi-L_desc-fl_mask.nii.gz → ...2NLin2009bAsym_hemi-L_desc-fl_mask.nii.gz
diff --git a/...2NLin2009bAsym_hemi-L_desc-ft_mask.nii.gz → ...2NLin2009bAsym_hemi-L_desc-ft_mask.nii.gz b/...2NLin2009bAsym_hemi-L_desc-ft_mask.nii.gz → ...2NLin2009bAsym_hemi-L_desc-ft_mask.nii.gz
diff --git a/...2009bAsym_hemi-L_desc-hfields_mask.nii.gz → ...2009bAsym_hemi-L_desc-hfields_mask.nii.gz b/...2009bAsym_hemi-L_desc-hfields_mask.nii.gz → ...2009bAsym_hemi-L_desc-hfields_mask.nii.gz
diff --git a/...NLin2009bAsym_hemi-R_desc-fct_mask.nii.gz → ...NLin2009bAsym_hemi-R_desc-fct_mask.nii.gz b/...NLin2009bAsym_hemi-R_desc-fct_mask.nii.gz → ...NLin2009bAsym_hemi-R_desc-fct_mask.nii.gz
diff --git a/...2NLin2009bAsym_hemi-R_desc-fl_mask.nii.gz → ...2NLin2009bAsym_hemi-R_desc-fl_mask.nii.gz b/...2NLin2009bAsym_hemi-R_desc-fl_mask.nii.gz → ...2NLin2009bAsym_hemi-R_desc-fl_mask.nii.gz
diff --git a/...2NLin2009bAsym_hemi-R_desc-ft_mask.nii.gz → ...2NLin2009bAsym_hemi-R_desc-ft_mask.nii.gz b/...2NLin2009bAsym_hemi-R_desc-ft_mask.nii.gz → ...2NLin2009bAsym_hemi-R_desc-ft_mask.nii.gz
diff --git a/...2009bAsym_hemi-R_desc-hfields_mask.nii.gz → ...2009bAsym_hemi-R_desc-hfields_mask.nii.gz b/...2009bAsym_hemi-R_desc-hfields_mask.nii.gz → ...2009bAsym_hemi-R_desc-hfields_mask.nii.gz
diff --git a/...52NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz → ...52NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz b/...52NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz → ...52NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz
diff --git a/...I152NLin6Asym_hemi-L_desc-fct_mask.nii.gz → ...I152NLin6Asym_hemi-L_desc-fct_mask.nii.gz b/...I152NLin6Asym_hemi-L_desc-fct_mask.nii.gz → ...I152NLin6Asym_hemi-L_desc-fct_mask.nii.gz
diff --git a/...NI152NLin6Asym_hemi-L_desc-fl_mask.nii.gz → ...NI152NLin6Asym_hemi-L_desc-fl_mask.nii.gz b/...NI152NLin6Asym_hemi-L_desc-fl_mask.nii.gz → ...NI152NLin6Asym_hemi-L_desc-fl_mask.nii.gz
diff --git a/...NI152NLin6Asym_hemi-L_desc-ft_mask.nii.gz → ...NI152NLin6Asym_hemi-L_desc-ft_mask.nii.gz b/...NI152NLin6Asym_hemi-L_desc-ft_mask.nii.gz → ...NI152NLin6Asym_hemi-L_desc-ft_mask.nii.gz
diff --git a/...NLin6Asym_hemi-L_desc-hfields_mask.nii.gz → ...NLin6Asym_hemi-L_desc-hfields_mask.nii.gz b/...NLin6Asym_hemi-L_desc-hfields_mask.nii.gz → ...NLin6Asym_hemi-L_desc-hfields_mask.nii.gz
diff --git a/...I152NLin6Asym_hemi-R_desc-fct_mask.nii.gz → ...I152NLin6Asym_hemi-R_desc-fct_mask.nii.gz b/...I152NLin6Asym_hemi-R_desc-fct_mask.nii.gz → ...I152NLin6Asym_hemi-R_desc-fct_mask.nii.gz
diff --git a/...NI152NLin6Asym_hemi-R_desc-fl_mask.nii.gz → ...NI152NLin6Asym_hemi-R_desc-fl_mask.nii.gz b/...NI152NLin6Asym_hemi-R_desc-fl_mask.nii.gz → ...NI152NLin6Asym_hemi-R_desc-fl_mask.nii.gz
diff --git a/...NI152NLin6Asym_hemi-R_desc-ft_mask.nii.gz → ...NI152NLin6Asym_hemi-R_desc-ft_mask.nii.gz b/...NI152NLin6Asym_hemi-R_desc-ft_mask.nii.gz → ...NI152NLin6Asym_hemi-R_desc-ft_mask.nii.gz
diff --git a/...NLin6Asym_hemi-R_desc-hfields_mask.nii.gz → ...NLin6Asym_hemi-R_desc-hfields_mask.nii.gz b/...NLin6Asym_hemi-R_desc-hfields_mask.nii.gz → ...NLin6Asym_hemi-R_desc-hfields_mask.nii.gz
diff --git a/...152NLin6Asym_res-04_desc-brain_T1w.nii.gz → ...152NLin6Asym_res-04_desc-brain_T1w.nii.gz b/...152NLin6Asym_res-04_desc-brain_T1w.nii.gz → ...152NLin6Asym_res-04_desc-brain_T1w.nii.gz
diff --git a/...a_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv → ...a_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv b/...a_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv → ...a_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv
diff --git a/dbsc/run.py → scattr/run.py b/dbsc/run.py → scattr/run.py
@@ -6,7 +6,7 @@
 
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
-    app = SnakeBidsApp("../dbsc", skip_parse_args=True)
+    app = SnakeBidsApp("../scattr", skip_parse_args=True)
     return app.parser
 
 

diff --git a/dbsc/workflow/Snakefile → scattr/workflow/Snakefile b/dbsc/workflow/Snakefile → scattr/workflow/Snakefile
diff --git a/dbsc/workflow/rules/freesurfer.smk → scattr/workflow/rules/freesurfer.smk b/dbsc/workflow/rules/freesurfer.smk → scattr/workflow/rules/freesurfer.smk
diff --git a/dbsc/workflow/rules/mrtpipelines.smk → scattr/workflow/rules/mrtpipelines.smk b/dbsc/workflow/rules/mrtpipelines.smk → scattr/workflow/rules/mrtpipelines.smk
diff --git a/dbsc/workflow/rules/zona_bb_subcortex.smk → scattr/workflow/rules/zona_bb_subcortex.smk b/dbsc/workflow/rules/zona_bb_subcortex.smk → scattr/workflow/rules/zona_bb_subcortex.smk
@@ -266,7 +266,7 @@ rule get_num_nodes:
     group:
         "subcortical_2"
     container:
-        config["singularity"]["dbsc"]
+        config["singularity"]["scattr"]
     script:
         "../scripts/zona_bb_subcortex/get_num_labels.py"
 
@@ -340,6 +340,6 @@ rule create_convex_hull:
     group:
         "subcortical_2"
     container:
-        config["singularity"]["dbsc"]
+        config["singularity"]["scattr"]
     script:
         "../scripts/zona_bb_subcortex/convexHull_roi.py"
diff --git a/...ripts/mrtpipelines/create_exclude_mask.py → ...ripts/mrtpipelines/create_exclude_mask.py b/...ripts/mrtpipelines/create_exclude_mask.py → ...ripts/mrtpipelines/create_exclude_mask.py
diff --git a/...w/scripts/mrtpipelines/create_roi_mask.py → ...w/scripts/mrtpipelines/create_roi_mask.py b/...w/scripts/mrtpipelines/create_roi_mask.py → ...w/scripts/mrtpipelines/create_roi_mask.py
diff --git a/...ripts/zona_bb_subcortex/convexHull_roi.py → ...ripts/zona_bb_subcortex/convexHull_roi.py b/...ripts/zona_bb_subcortex/convexHull_roi.py → ...ripts/zona_bb_subcortex/convexHull_roi.py
diff --git a/...ripts/zona_bb_subcortex/get_num_labels.py → ...ripts/zona_bb_subcortex/get_num_labels.py b/...ripts/zona_bb_subcortex/get_num_labels.py → ...ripts/zona_bb_subcortex/get_num_labels.py