ENH: Add flip, inv, mt, and part entities (#688)

* Add new entity patterns. * Incorporate part into path patterns. This involves splitting the phase suffix from the bold, cbv, and sbref suffixes. * Update nodot file too.
bids-standard · Dec 19, 2020 · 11f665b · 11f665b
1 parent 0d14325
commit 11f665b
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Showing 2 changed files with 36 additions and 3 deletions.
diff --git a/bids/layout/config/bids-nodot.json b/bids/layout/config/bids-nodot.json
@@ -49,6 +49,22 @@
             "name": "echo",
             "pattern": "[_/\\\\]+echo-([0-9]+)"
         },
+        {
+            "name": "flip",
+            "pattern": "[_/\\\\]+flip-([0-9]+)"
+        },
+        {
+            "name": "inv",
+            "pattern": "[_/\\\\]+inv-([0-9]+)"
+        },
+        {
+            "name": "mt",
+            "pattern": "[_/\\\\]+mt-(on|off)"
+        },
+        {
+            "name": "part",
+            "pattern": "[_/\\\\]+part-(imag|mag|phase|real)"
+        },
         {
             "name": "recording",
             "pattern": "[_/\\\\]+recording-([a-zA-Z0-9]+)"

diff --git a/bids/layout/config/bids.json b/bids/layout/config/bids.json
@@ -49,6 +49,22 @@
             "name": "echo",
             "pattern": "[_/\\\\]+echo-([0-9]+)"
         },
+        {
+            "name": "flip",
+            "pattern": "[_/\\\\]+flip-([0-9]+)"
+        },
+        {
+            "name": "inv",
+            "pattern": "[_/\\\\]+inv-([0-9]+)"
+        },
+        {
+            "name": "mt",
+            "pattern": "[_/\\\\]+mt-(on|off)"
+        },
+        {
+            "name": "part",
+            "pattern": "[_/\\\\]+part-(imag|mag|phase|real)"
+        },
         {
             "name": "recording",
             "pattern": "[_/\\\\]+recording-([a-zA-Z0-9]+)"
@@ -80,10 +96,11 @@
     ],
 
     "default_path_patterns": [
-        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
         "sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",