From 51dca03584ca31c21fec088e6aaef24b4f1166b8 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Mon, 23 Oct 2023 19:36:50 -0400
Subject: [PATCH] ENH: Add hemi entity to transform path patterns

---
 niworkflows/data/nipreps.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/niworkflows/data/nipreps.json b/niworkflows/data/nipreps.json
index 61bbedc9e7e..01f32f20011 100644
--- a/niworkflows/data/nipreps.json
+++ b/niworkflows/data/nipreps.json
@@ -153,14 +153,14 @@
   ],
   "default_path_patterns": [
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<white|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/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}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_hemi-{hemi<L|R>}]_from-{from}_to-{to}_mode-{mode<image|points>|image}[_desc-{desc}]_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<AROMAnoiseICs>|AROMAnoiseICs}{extension<.csv|.tsv>|.csv}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}",