Move hemi entity before space (PennLINC#1287)

tsalo · Oct 9, 2024 · f54208a · f54208a
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diff --git 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
@@ -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
@@ -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>}",