[ENH] Add ReconScalars node to recon workflows (#683)

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
PennLINC · Feb 1, 2024 · 862fe30 · 862fe30
1 parent af57c4b
commit 862fe30
Showing 15 changed files with 786 additions and 52 deletions.
diff --git a/.circleci/ScalarMapper.sh b/.circleci/ScalarMapper.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+cat << DOC
+
+Test the TORTOISE recon workflow
+=================================
+
+All supported reconstruction workflows get tested
+
+
+Inputs:
+-------
+ - qsiprep multi shell results (data/DSDTI_fmap)
+
+DOC
+set +e
+source ./get_data.sh
+TESTDIR=${PWD}
+TESTNAME=scalar_mapper_test
+get_config_data ${TESTDIR}
+get_bids_data ${TESTDIR} multishell_output
+CFG=${TESTDIR}/data/nipype.cfg
+
+# Test MRtrix3 multishell msmt with ACT
+setup_dir ${TESTDIR}/${TESTNAME}
+TEMPDIR=${TESTDIR}/${TESTNAME}/work
+OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
+BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsiprep
+export FS_LICENSE=${TESTDIR}/data/license.txt
+QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
+
+${QSIPREP_CMD} \
+   -w ${TEMPDIR} \
+	--recon-input ${BIDS_INPUT_DIR} \
+	--sloppy \
+    --stop-on-first-crash \
+	--recon-spec bundle_scalar_map \
+	--recon-only \
+	-vv
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -272,6 +272,18 @@ jobs:
             cd .circleci
             bash PyAFQReconExternalTrk.sh
 
+  Recon_ScalarMap:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - run: *runinstall
+      - run:
+          name: Test scalar_mapping workflow
+          no_output_timeout: 1h
+          command: |
+            cd .circleci
+            bash ScalarMapper.sh
+
   Recon_AMICO:
     <<: *dockersetup
     resource_class: medium+
@@ -319,7 +331,7 @@ jobs:
               echo "the command ``git fetch --tags --verbose`` and push"
               echo "them to your fork with ``git push origin --tags``"
             fi
-            sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/qsiprep_docker.py
+            sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" wrapper/qsiprep-container/qsiprep_docker.py
             sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'${CIRCLE_TAG:-$THISVERSION}'/" docs/citing.rst
             sed -i "s/title = {qsiprep}/title = {qsiprep ${CIRCLE_TAG:-$THISVERSION}}/" qsiprep/data/boilerplate.bib
             # Build docker image
@@ -609,6 +621,13 @@ workflows:
             tags:
               only: /.*/
 
+      - Recon_ScalarMap:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/
+
       - deployable:
           requires:
             - build_docs
@@ -630,6 +649,7 @@ workflows:
             - Recon_AMICO
             - Recon_PYAFQ
             - Recon_PYAFQExternalTrk
+            - Recon_ScalarMap
           filters:
             branches:
               only: master

diff --git a/qsiprep/data/pipelines/bundle_scalar_map.json b/qsiprep/data/pipelines/bundle_scalar_map.json
@@ -0,0 +1,55 @@
+{
+  "name": "bundle_scalar_map",
+  "space" : "T1w",
+  "atlases": [ ],
+  "anatomical": [ ],
+  "nodes": [
+    {
+      "name": "DIPYdki",
+      "software": "Dipy",
+      "action": "DKI_reconstruction",
+      "input": "qsiprep",
+      "output_suffix": "DKI",
+      "parameters": {
+        "write_mif": false,
+        "write_fibgz": false
+      }
+    },
+    {
+      "name": "dsistudio_gqi",
+      "software": "DSI Studio",
+      "action": "reconstruction",
+      "input": "qsiprep",
+      "output_suffix": "gqi",
+      "parameters": {"method": "gqi"}
+    },
+    {
+      "name": "autotrackgqi",
+      "software": "DSI Studio",
+      "action": "autotrack",
+      "input": "dsistudio_gqi",
+      "output_suffix": "AutoTrackGQI",
+      "parameters": {
+        "track_id": "Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus",
+        "tolerance": "22,26,30",
+        "track_voxel_ratio": 2.0,
+        "yield_rate": 0.000001
+      }
+    },
+    {
+      "name": "gqi_scalars",
+      "software": "DSI Studio",
+      "action": "export",
+      "input": "dsistudio_gqi",
+      "output_suffix": "gqiscalar"
+    },
+    {
+      "name": "bundle_means",
+      "software": "qsiprep",
+      "action": "bundle_map",
+      "input": "autotrackgqi",
+      "scalars_from": ["gqi_scalars", "DIPYdki"],
+      "output_suffix": "bundlemap"
+    }
+  ]
+}
diff --git a/qsiprep/interfaces/interchange.py b/qsiprep/interfaces/interchange.py
@@ -48,6 +48,7 @@ class _ReconWorkflowInputsInputSpec(BaseInterfaceInputSpec):
 class _ReconWorkflowInputsOutputSpec(TraitedSpec):
     pass
 
+
 class ReconWorkflowInputs(SimpleInterface):
     input_spec = _ReconWorkflowInputsInputSpec
     output_spec = _ReconWorkflowInputsOutputSpec
@@ -83,4 +84,4 @@ def _run_interface(self, runtime):
 
 for name in anatomical_workflow_outputs:
     _ReconAnatomicalDataInputSpec.add_class_trait(name, traits.Any)
-    _ReconAnatomicalDataOutputSpec.add_class_trait(name, traits.Any)
+    _ReconAnatomicalDataOutputSpec.add_class_trait(name, traits.Any)