[ENH] Update pyafq; add pyafq full test (#533)

.circleci/PyAFQReconTests.sh

@@ -26,8 +26,8 @@ EDDY_CFG=${TESTDIR}/data/eddy_config.json
 export FS_LICENSE=${TESTDIR}/data/license.txt
 
 
-# Test pyAFQ_full
-TESTNAME=pyafq_input_trk_test
+# Test pyafq_tractometry
+TESTNAME=pyafq_tractometry_test
 setup_dir ${TESTDIR}/${TESTNAME}
 TEMPDIR=${TESTDIR}/${TESTNAME}/work
 OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
@@ -38,6 +38,23 @@ ${QSIPREP_CMD}  \
 	 -w ${TEMPDIR} \
 	 --recon-input ${BIDS_INPUT_DIR} \
 	 --sloppy \
-	 --recon-spec pyafq_input_trk \
+	 --recon-spec pyafq_tractometry \
 	 --recon-only \
 	 -vv
+
+
+# Test mrtrix_multishell_msmt_pyafq_tractometry
+TESTNAME=mrtrix_multishell_msmt_pyafq_tractometry_test
+setup_dir ${TESTDIR}/${TESTNAME}
+TEMPDIR=${TESTDIR}/${TESTNAME}/work
+OUTPUT_DIR=${TESTDIR}/${TESTNAME}/derivatives
+BIDS_INPUT_DIR=${TESTDIR}/data/multishell_output/qsiprep
+QSIPREP_CMD=$(run_qsiprep_cmd ${BIDS_INPUT_DIR} ${OUTPUT_DIR})
+
+${QSIPREP_CMD}  \
+	 -w ${TEMPDIR} \
+	 --recon-input ${BIDS_INPUT_DIR} \
+	 --sloppy \
+	 --recon-spec mrtrix_multishell_msmt_pyafq_tractometry \
+	 --recon-only \
+	 -vv

docs/reconstruction.rst

@@ -288,7 +288,7 @@ used for tractography with no T1w-based anatomical constraints.
 
 .. _pyafq:
 
-``pyafq``
+``pyafq_tractometry``
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 This workflow uses the AFQ [Yeatman2012]_ implemented in Python [Kruper2021]_ to recognize
@@ -297,11 +297,13 @@ those pathways. See the `pyAFQ documentation <https://yeatmanlab.github.io/pyAFQ
 
 .. _pyafq_input_trk:
 
-``pyafq_input_trk``
+``mrtrix_multishell_msmt_pyafq_tractometry``
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Identical to :ref:`pyafq` except that tractography generated using another reconstruciton pipeline
-(such as MRTrix3), instead of using pyAFQ's default DIPY tractography.
+Identical to :ref:`pyafq` except that tractography generated using IFOD2 from MRTrix3,
+instead of using pyAFQ's default DIPY tractography.
+This can also be used as an example for how to import tractographies from other
+reconstruciton pipelines to pyAFQ.
 
 
 .. _amico_noddi:

qsiprep/data/pipelines/pyafq_input_trk.json → qsiprep/data/pipelines/mrtrix_multishell_msmt_pyafq_tractometry.json

@@ -1,7 +1,7 @@
 {
     "description": "Use pyAFQ to perform the Tractometry pipeline, with tractography from qsiprep",
     "space": "T1w",
-    "name": "pyAFQ_import_trk",
+    "name": "mrtrix_multishell_msmt_pyafq_tractometry",
     "atlases": [],
     "nodes": [
         {
@@ -41,13 +41,14 @@
             }
         },
         {
-            "name": "pyAFQ_full",
+            "name": "pyafq_tractometry",
             "software": "pyAFQ",
-            "action": "pyAFQ_full",
+            "action": "pyafq_tractometry",
             "input": "track_ifod2",
-            "output_suffix": "PYAFQ_FULL_ET",
+            "output_suffix": "PYAFQ_TRACTOMETRY_ET",
             "parameters": {
                 "use_external_tracking": true,
+                "export": "all",
                 "directions": "prob",
                 "max_angle": 30.0,
                 "sphere": "",
@@ -59,8 +60,8 @@
                 "stop_mask": "",
                 "stop_threshold": 0,
                 "step_size": 0.5,
-                "min_length": 10,
-                "max_length": 1000,
+                "min_length": 50,
+                "max_length": 250,
                 "odf_model": "CSD",
                 "tracker": "local",
                 "nb_points": false,
@@ -89,7 +90,7 @@
                 "save_intermediates": "",
                 "n_points": 100,
                 "clean_rounds": 5,
-                "distance_threshold": 5,
+                "distance_threshold": 3,
                 "length_threshold": 4,
                 "min_sl": 20,
                 "stat": "mean",

qsiprep/data/pipelines/pyafq.json → qsiprep/data/pipelines/pyafq_tractometry.json

@@ -1,17 +1,18 @@
 {
     "description": "Use pyAFQ to perform the full Tractometry pipeline",
     "space": "T1w",
-    "name": "pyAFQ_full",
+    "name": "pyafq_tractometry",
     "atlases": [],
     "nodes": [
         {
-            "name": "pyAFQ_full",
+            "name": "pyafq_tractometry",
             "software": "pyAFQ",
-            "action": "pyAFQ_full",
+            "action": "pyafq_tractometry",
             "input": "qsiprep",
-            "output_suffix": "PYAFQ_FULL",
+            "output_suffix": "PYAFQ_TRACTOMETRY",
             "parameters": {
                 "use_external_tracking": false,
+                "export": "all",
                 "directions": "prob",
                 "max_angle": 30.0,
                 "sphere": "",
@@ -23,8 +24,8 @@
                 "stop_mask": "",
                 "stop_threshold": 0,
                 "step_size": 0.5,
-                "min_length": 10,
-                "max_length": 1000,
+                "min_length": 50,
+                "max_length": 250,
                 "odf_model": "CSD",
                 "tracker": "local",
                 "nb_points": false,
@@ -53,7 +54,7 @@
                 "save_intermediates": "",
                 "n_points": 100,
                 "clean_rounds": 5,
-                "distance_threshold": 5,
+                "distance_threshold": 3,
                 "length_threshold": 4,
                 "min_sl": 20,
                 "stat": "mean",

qsiprep/interfaces/pyafq.py

@@ -56,8 +56,6 @@ def _run_interface(self, runtime):
                                    newpath=shim_dir)
         mask_file = fname_presuffix(self.inputs.mask_file,
                                     newpath=shim_dir)
-        tck_file = fname_presuffix(self.inputs.tck_file,
-                                   newpath=shim_dir)
         itk_file = fname_presuffix(self.inputs.itk_file,
                                    newpath=shim_dir)
         os.symlink(self.inputs.bval_file, bval_file)
@@ -69,6 +67,8 @@ def _run_interface(self, runtime):
         kwargs = self.inputs.kwargs
 
         if self.inputs.tck_file and isdefined(self.inputs.tck_file):
+            tck_file = fname_presuffix(self.inputs.tck_file,
+                                    newpath=shim_dir)
             os.symlink(self.inputs.tck_file, tck_file)
         else:
             tck_file = None
@@ -77,16 +77,13 @@ def _run_interface(self, runtime):
 
         if tck_file is None:
             tck_file = kwargs['import_tract']
-        else:
-            kwargs.pop('import_tract', None)
+        kwargs.pop('import_tract', None)
         if brain_mask_definition is None:
             brain_mask_definition = kwargs['brain_mask_definition']
-        else:
-            kwargs.pop('brain_mask_definition', None)
-        if itk_map is None:
-            itk_map = kwargs['mapping_definition']
-        else:
-            kwargs.pop('mapping_definition', None)
+        kwargs.pop('brain_mask_definition', None)
+        # if itk_map is None:  # Use pyAFQ internal mapping
+        #     itk_map = kwargs['mapping_definition']
+        # kwargs.pop('mapping_definition', None)
 
         if 'parallel_segmentation' in kwargs:
             if 'n_jobs' not in kwargs['parallel_segmentation']\
@@ -102,7 +99,7 @@ def _run_interface(self, runtime):
             dwi_file, bval_file, bvec_file, output_dir,
             import_tract=tck_file,
             brain_mask_definition=brain_mask_definition,
-            mapping_definition=itk_map,
+            # mapping_definition=itk_map,
             **kwargs)
         myafq.export("profiles")
 

qsiprep/workflows/recon/build_workflow.py

@@ -212,7 +212,7 @@ def workflow_from_spec(omp_nthreads, available_anatomical_data, node_spec,
             return init_amico_noddi_fit_wf(**kwargs)
 
     elif software == "pyAFQ":
-        if node_spec["action"] == "pyAFQ_full":
+        if node_spec["action"] == "pyafq_tractometry":
             return init_pyafq_wf(**kwargs)
 
     # qsiprep operations

setup.cfg

@@ -54,7 +54,7 @@ install_requires =
     scikit-learn >=0.20.2
     scikit-image
     SimpleITK
-    pyAFQ >= 0.12
+    pyAFQ >= 1.0.1
 test_requires =
     coverage
     codecov