From f54208aedf4512fadc09d2364499ac68880e6773 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Wed, 9 Oct 2024 13:33:27 -0400
Subject: [PATCH] Move hemi entity before space (#1287)

---
 docs/outputs.rst                              | 24 +++++++++----------
 docs/usage.rst                                | 14 +++++------
 xcp_d/data/xcp_d_bids_config.json             | 12 +++++-----
 xcp_d/data/xcp_d_bids_config2.json            | 12 +++++-----
 xcp_d/tests/data/test_pnc_cifti_outputs.txt   | 20 ++++++++--------
 .../data/test_pnc_cifti_t2wonly_outputs.txt   | 20 ++++++++--------
 xcp_d/tests/test_utils_bids.py                | 24 +++++++++----------
 xcp_d/tests/test_workflows_anatomical.py      |  7 ++++--
 8 files changed, 68 insertions(+), 65 deletions(-)

diff --git a/docs/outputs.rst b/docs/outputs.rst
index 98f086068..542d0968c 100644
--- a/docs/outputs.rst
+++ b/docs/outputs.rst
@@ -133,27 +133,27 @@ brain.
    xcp_d/
       sub-<label>/[ses-<label>/]
          anat/
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_midthickness.surf.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_inflated.surf.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_vinflated.surf.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_pial.surf.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_smoothwm.surf.gii
+            <source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii
+            <source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_inflated.surf.gii
+            <source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii
+            <source_entities>_hemi-<L|R>_space-fsLR_den-32k_pial.surf.gii
+            <source_entities>_hemi-<L|R>_space-fsLR_den-32k_white.surf.gii
 
 
 Surface morphometric files
 ==========================
 
 *XCP-D* will also pass along several morphometric files from the preprocessing derivatives,
-as long as the files are already in fsLR space at 32k density.
+as long as the files are already in fsLR space at 91k density.
 
 .. code-block::
 
    xcp_d/
       sub-<label>/[ses-<label>/]
          anat/
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_sulc.shape.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_curv.shape.gii
-            <source_entities>_space-fsLR_den-32k_hemi-<L|R>_thickness.shape.gii
+            <source_entities>_space-fsLR_den-91k_sulc.dscalar.nii
+            <source_entities>_space-fsLR_den-91k_curv.dscalar.nii
+            <source_entities>_space-fsLR_den-91k_thickness.dscalar.nii
 
 
 *XCP-D* will additionally parcellate each of these files, when they are present, using each of the
@@ -164,9 +164,9 @@ atlases it uses to parcellate the functional outputs.
    xcp_d/
       sub-<label>/[ses-<label>/]
          anat/
-            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-curv_morph.tsv
-            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-sulc_morph.tsv
-            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-thickness_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_stat-mean_desc-curv_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_stat-mean_desc-sulc_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_stat-mean_desc-thickness_morph.tsv
 
 
 ******************
diff --git a/docs/usage.rst b/docs/usage.rst
index d2e935ab4..86d85adce 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -115,25 +115,25 @@ Command-Line Arguments
 
          *  -  Filename
             -  Description
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_pial.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_pial.surf.gii``
             -  The gray matter / pial matter border.
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_smoothwm.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_white.surf.gii``
             -  The smoothed gray matter / white matter border for the cortex.
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_midthickness.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_midthickness.surf.gii``
             -  The midpoints between wm and pial surfaces.
                This is derived from the FreeSurfer graymid
                (``mris_expand`` with distance=0.5 applied to the WM surfs).
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_inflated.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_inflated.surf.gii``
             -  An inflation of the midthickness surface (useful for visualization).
                This file is only created if the input type is "hcp" or "dcan".
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_midthickness.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii``
             -  The midpoints between wm and pial surfaces.
                This is created by averaging the coordinates from the wm and pial surfaces.
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_inflated.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_inflated.surf.gii``
             -  An inflation of the midthickness surface (useful for visualization).
                This is derived from the HCP midthickness file.
                This file is only created if the input type is "fmriprep" or "nibabies".
-         *  -  ``<source_entities>_space-fsLR_den-32k_hemi-<L|R>_desc-hcp_vinflated.surf.gii``
+         *  -  ``<source_entities>_hemi-<L|R>_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii``
             -  A very-inflated midthicknesss surface (also for visualization).
                This is derived from the HCP midthickness file.
                This file is only created if the input type is "fmriprep" or "nibabies".
diff --git a/xcp_d/data/xcp_d_bids_config.json b/xcp_d/data/xcp_d_bids_config.json
index 80039531e..06cc4ce50 100755
--- a/xcp_d/data/xcp_d_bids_config.json
+++ b/xcp_d/data/xcp_d_bids_config.json
@@ -25,7 +25,7 @@
     "atlases/atlas-{atlas}/atlas-{atlas}[_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|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}][_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}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}]_hemi-{hemi<L|R>}[_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
+    "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}][_seg-{segmentation}][_den-{den}][_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_desc-{desc}]_{suffix<sulc|curv|thickness|myelinw>}{extension<.dscalar.nii|.json>|.dscalar.nii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_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}][_seg-{segmentation}][_res-{res}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
@@ -40,11 +40,11 @@
     "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}][_desc-{desc}]_{suffix<motion|outliers>}{extension<.json|.tsv>|.tsv}",
     "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}][_space-{space}][_cohort-{cohort}][_res-{res}][_den-{den}][_desc-{desc}]_{suffix<qc>}{extension<.tsv|.json>|.tsv}",
     "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}][_desc-{desc}]_{suffix<qc>}{extension<.hdf5>|.hdf5}",
-    "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}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.dscalar.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.ptseries.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pscalar.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pconn.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.dscalar.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.ptseries.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pscalar.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pconn.nii|.json>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|motion>}{extension<.html|.svg|.png>}",
diff --git a/xcp_d/data/xcp_d_bids_config2.json b/xcp_d/data/xcp_d_bids_config2.json
index 20ff97979..399270885 100755
--- a/xcp_d/data/xcp_d_bids_config2.json
+++ b/xcp_d/data/xcp_d_bids_config2.json
@@ -21,7 +21,7 @@
     "atlases/atlas-{atlas}/atlas-{atlas}[_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|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}][_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}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}]_hemi-{hemi<L|R>}[_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
+    "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}][_seg-{segmentation}][_den-{den}][_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_desc-{desc}]_{suffix<sulc|curv|thickness|myelinw>}{extension<.dscalar.nii|.json>|.dscalar.nii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_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}][_seg-{segmentation}][_res-{res}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
@@ -36,11 +36,11 @@
     "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}][_desc-{desc}]_{suffix<motion|outliers>}{extension<.json|.tsv>|.tsv}",
     "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}][_space-{space}][_cohort-{cohort}][_res-{res}][_den-{den}][_desc-{desc}]_{suffix<qc>}{extension<.tsv|.json>|.tsv}",
     "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}][_desc-{desc}]_{suffix<qc>}{extension<.hdf5>|.hdf5}",
-    "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}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.dscalar.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.ptseries.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pscalar.nii|.json>}",
-    "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}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pconn.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.dscalar.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.ptseries.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pscalar.nii|.json>}",
+    "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}][_hemi-{hemi<L|R>}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pconn.nii|.json>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|motion>}{extension<.html|.svg|.png>}",
diff --git a/xcp_d/tests/data/test_pnc_cifti_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_outputs.txt
index 90c1e7e43..65ec2eec2 100644
--- a/xcp_d/tests/data/test_pnc_cifti_outputs.txt
+++ b/xcp_d/tests/data/test_pnc_cifti_outputs.txt
@@ -23,16 +23,16 @@ sub-1648798153.html
 sub-1648798153/ses-PNC1
 sub-1648798153/ses-PNC1/anat
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_inflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_midthickness.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_vinflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_pial.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_white.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_inflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_midthickness.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_vinflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_pial.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_white.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_inflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_pial.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_white.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_inflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_pial.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_white.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_curv.dscalar.nii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_sulc.dscalar.nii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_thickness.dscalar.nii
diff --git a/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
index 45f6ccebb..cf4f842f8 100644
--- a/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
+++ b/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
@@ -19,16 +19,16 @@ sub-1648798153.html
 sub-1648798153/ses-PNC1
 sub-1648798153/ses-PNC1/anat
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_desc-preproc_T2w.nii.gz
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_inflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_midthickness.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_vinflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_pial.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_white.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_inflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_midthickness.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_desc-hcp_vinflated.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_pial.surf.gii
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-R_white.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_inflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_pial.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_white.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_inflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_midthickness.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_desc-hcp_vinflated.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_pial.surf.gii
+sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_white.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_curv.dscalar.nii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_sulc.dscalar.nii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-91k_thickness.dscalar.nii
diff --git a/xcp_d/tests/test_utils_bids.py b/xcp_d/tests/test_utils_bids.py
index ab72ad610..b6c44f4d0 100644
--- a/xcp_d/tests/test_utils_bids.py
+++ b/xcp_d/tests/test_utils_bids.py
@@ -148,10 +148,10 @@ def test_collect_mesh_data(datasets, tmp_path_factory):
     )
     os.makedirs(std_mesh_dir / "sub-1648798153/ses-PNC1/anat", exist_ok=True)
     files = [
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-L_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-L_white.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-R_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-R_white.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-L_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-L_space-fsLR_den-32k_white.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-R_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-R_space-fsLR_den-32k_white.surf.gii",
     ]
     for f in files:
         (std_mesh_dir / "sub-1648798153/ses-PNC1/anat").joinpath(f).touch()
@@ -171,14 +171,14 @@ def test_collect_mesh_data(datasets, tmp_path_factory):
     )
     os.makedirs(bad_mesh_dir / "sub-1648798153/ses-PNC1/anat", exist_ok=True)
     files = [
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-L_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-L_white.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-R_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_space-fsLR_den-32k_hemi-R_white.surf.gii",
-        "sub-1648798153_ses-PNC1_acq-test_space-fsLR_den-32k_hemi-L_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_acq-test_space-fsLR_den-32k_hemi-L_white.surf.gii",
-        "sub-1648798153_ses-PNC1_acq-test_space-fsLR_den-32k_hemi-R_pial.surf.gii",
-        "sub-1648798153_ses-PNC1_acq-test_space-fsLR_den-32k_hemi-R_white.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-L_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-L_space-fsLR_den-32k_white.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-R_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_hemi-R_space-fsLR_den-32k_white.surf.gii",
+        "sub-1648798153_ses-PNC1_acq-test_hemi-L_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_acq-test_hemi-L_space-fsLR_den-32k_white.surf.gii",
+        "sub-1648798153_ses-PNC1_acq-test_hemi-R_space-fsLR_den-32k_pial.surf.gii",
+        "sub-1648798153_ses-PNC1_acq-test_hemi-R_space-fsLR_den-32k_white.surf.gii",
     ]
     for f in files:
         (std_mesh_dir / "sub-1648798153/ses-PNC1/anat").joinpath(f).touch()
diff --git a/xcp_d/tests/test_workflows_anatomical.py b/xcp_d/tests/test_workflows_anatomical.py
index 56cbe034b..b55fea32a 100644
--- a/xcp_d/tests/test_workflows_anatomical.py
+++ b/xcp_d/tests/test_workflows_anatomical.py
@@ -37,8 +37,11 @@ def surface_files(datasets, tmp_path_factory):
         std_fref = fref.replace("native_", "fsLR_")
         std_fname = os.path.basename(fpath)
         std_fname = std_fname.replace(
-            "sub-1648798153_ses-PNC1_acq-refaced_",
-            "sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_",
+            "sub-1648798153_ses-PNC1_acq-refaced_hemi-L_",
+            "sub-1648798153_ses-PNC1_acq-refaced_hemi-L_space-fsLR_den-32k_",
+        ).replace(
+            "sub-1648798153_ses-PNC1_acq-refaced_hemi-R_",
+            "sub-1648798153_ses-PNC1_acq-refaced_hemi-R_space-fsLR_den-32k_",
         )
         std_fpath = os.path.join(tmpdir, std_fname)
         shutil.copyfile(fpath, std_fpath)