From 16609f2bf40e5745898bfccc3ec6d723369d871d Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Thu, 30 Nov 2023 11:24:43 -0500
Subject: [PATCH] Add ASL support (#839)

* Add "asl" to list of non-standard spaces.

* Add "asl" to data collection.

* Add ASL-related filename patterns to config.

* Drop m0scan from fmap pattern.
---
 niworkflows/data/nipreps.json  | 6 +++++-
 niworkflows/interfaces/bids.py | 3 ++-
 niworkflows/utils/bids.py      | 1 +
 niworkflows/utils/spaces.py    | 1 +
 4 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json
index 01f32f20011..1143dc7f601 100644
--- a/niworkflows/data/nipreps.json
+++ b/niworkflows/data/nipreps.json
@@ -87,7 +87,7 @@
     },
     {
       "name": "datatype",
-      "pattern": "[/\\\\]+(func|anat|fmap|dwi|meg|eeg|figures)[/\\\\]+"
+      "pattern": "[/\\\\]+(func|anat|fmap|dwi|meg|eeg|perf|figures)[/\\\\]+"
     },
     {
       "name": "extension",
@@ -172,6 +172,10 @@
     "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}{extension<.tsv|.bval|.bvec|.b>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_{suffix<aslcontext>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries>}{extension<.json|.tsv>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|att|cbf|coverage|mask>}{extension<.nii|.nii.gz|.json|.tsv>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|T2starw|MTw|TSE>}{extension<.html|.svg>|.svg}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_fmapid-{fmapid}][_desc-{desc}]_{suffix<fieldmap>}{extension<.html|.svg>|.svg}",
diff --git a/niworkflows/interfaces/bids.py b/niworkflows/interfaces/bids.py
index 409831f75a6..21a4e43f4a0 100644
--- a/niworkflows/interfaces/bids.py
+++ b/niworkflows/interfaces/bids.py
@@ -227,6 +227,7 @@ class _BIDSDataGrabberOutputSpec(TraitedSpec):
     flair = OutputMultiObject(desc="output FLAIR images")
     pet = OutputMultiObject(desc="output PET images")
     dwi = OutputMultiObject(desc="output DWI images")
+    asl = OutputMultiObject(desc="output ASL images")
 
 
 class BIDSDataGrabber(SimpleInterface):
@@ -278,7 +279,7 @@ def _run_interface(self, runtime):
                 )
             )
 
-        for imtype in ["bold", "t2w", "flair", "fmap", "sbref", "roi", "pet"]:
+        for imtype in ["bold", "t2w", "flair", "fmap", "sbref", "roi", "pet", "asl"]:
             if not bids_dict[imtype]:
                 LOGGER.info(
                     'No "%s" images found for sub-%s', imtype, self.inputs.subject_id
diff --git a/niworkflows/utils/bids.py b/niworkflows/utils/bids.py
index c642ef5fd1e..fdcfbd586f3 100644
--- a/niworkflows/utils/bids.py
+++ b/niworkflows/utils/bids.py
@@ -40,6 +40,7 @@
     "sbref": {"datatype": "func", "suffix": "sbref", "part": ["mag", None]},
     "t1w": {"datatype": "anat", "suffix": "T1w", "part": ["mag", None]},
     "t2w": {"datatype": "anat", "suffix": "T2w", "part": ["mag", None]},
+    "asl": {"datatype": "perf", "suffix": "asl"},
 }
 
 
diff --git a/niworkflows/utils/spaces.py b/niworkflows/utils/spaces.py
index 2f014ccbd21..5fddda253a4 100644
--- a/niworkflows/utils/spaces.py
+++ b/niworkflows/utils/spaces.py
@@ -38,6 +38,7 @@
     "session",
     "individual",
     "dwi",
+    "asl",
 ]
 """List of supported nonstandard reference spaces."""