From c1382666f88ad9eeaabd8ce345c62dcaaf3d6e76 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 19 Nov 2024 16:32:20 -0500
Subject: [PATCH 1/3] Hardcode hsvs probseg space as ACPC, not T1w

---
 qsirecon/workflows/recon/anatomical.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qsirecon/workflows/recon/anatomical.py b/qsirecon/workflows/recon/anatomical.py
index 97e8f17f..e9861fab 100644
--- a/qsirecon/workflows/recon/anatomical.py
+++ b/qsirecon/workflows/recon/anatomical.py
@@ -135,7 +135,7 @@ def init_highres_recon_anatomical_wf(
             DerivativesDataSink(
                 dismiss_entities=("desc",),
                 seg="hsvs",
-                space="T1w",
+                space="ACPC",
                 suffix="probseg",
                 extension=".nii.gz",
                 compress=True,

From fe84a49bb817549f9ab4973c402b94592482145e Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 19 Nov 2024 16:39:53 -0500
Subject: [PATCH 2/3] Address remaining space mislabels.

---
 docs/connectivity_matrices.rst                            | 8 ++++----
 docs/nonscalars/dsistudio_autotrack.csv                   | 8 ++++----
 docs/nonscalars/dsistudio_gqi.csv                         | 6 +++---
 docs/nonscalars/mrtrix_anat.csv                           | 2 +-
 docs/nonscalars/ss3t_autotrack.csv                        | 8 ++++----
 qsirecon/data/nonscalars/mrtrix_anat.yaml                 | 2 +-
 qsirecon/interfaces/mrtrix.py                             | 2 +-
 qsirecon/interfaces/scalar_mapping.py                     | 5 ++++-
 .../tests/data/mrtrix_multishell_msmt_hsvs_outputs.txt    | 2 +-
 qsirecon/workflows/recon/utils.py                         | 1 -
 10 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/docs/connectivity_matrices.rst b/docs/connectivity_matrices.rst
index 7a21d386..03b46050 100644
--- a/docs/connectivity_matrices.rst
+++ b/docs/connectivity_matrices.rst
@@ -76,10 +76,10 @@ associated reconstruction workflows dataset.
          qsirecon-<suffix>/
             sub-<label>/
                dwi/
-                  sub-<label>_space-T1w_seg-<label>_dseg.nii.gz
-                  sub-<label>_space-T1w_seg-<label>_dseg.mif.gz
-                  sub-<label>_space-T1w_seg-<label>_dseg.json
-                  sub-<label>_space-T1w_seg-<label>_dseg.tsv
+                  sub-<label>_space-ACPC_seg-<label>_dseg.nii.gz
+                  sub-<label>_space-ACPC_seg-<label>_dseg.mif.gz
+                  sub-<label>_space-ACPC_seg-<label>_dseg.json
+                  sub-<label>_space-ACPC_seg-<label>_dseg.tsv
 
 
 .. _custom_atlases:
diff --git a/docs/nonscalars/dsistudio_autotrack.csv b/docs/nonscalars/dsistudio_autotrack.csv
index a13fbba3..16b67cfa 100644
--- a/docs/nonscalars/dsistudio_autotrack.csv
+++ b/docs/nonscalars/dsistudio_autotrack.csv
@@ -1,5 +1,5 @@
-\*_streamlines.tck.gz,One tck.gz per bundle. The bundle represented by this file is specified in the ``bundle-`` tag. 
-\*bundles-DSIStudio\*_scalarstats.csv,Statistics on scalars produced by this workflow 
+\*_streamlines.tck.gz,One tck.gz per bundle. The bundle represented by this file is specified in the ``bundle-`` tag.
+\*bundles-DSIStudio\*_scalarstats.csv,Statistics on scalars produced by this workflow
 \*bundles-DSIStudio\*_tdistats.tsv,Statistics on streamline density in voxels
-\*space-T1w\*_dwimap.fib.gz,DSI Studio fib format containing the GQI ODFs used for AutoTrack. 
-\*space-T1w\*_mapping.map.gz,Mapping file produced by DSI Studio.
+\*space-ACPC\*_dwimap.fib.gz,DSI Studio fib format containing the GQI ODFs used for AutoTrack.
+\*space-ACPC\*_mapping.map.gz,Mapping file produced by DSI Studio.
diff --git a/docs/nonscalars/dsistudio_gqi.csv b/docs/nonscalars/dsistudio_gqi.csv
index 9c5a65f4..483a92dc 100644
--- a/docs/nonscalars/dsistudio_gqi.csv
+++ b/docs/nonscalars/dsistudio_gqi.csv
@@ -1,3 +1,3 @@
-\*_connectivity.mat,MATLAB format mat file containing connectivity matrices for all the selected atlases. This is an hdf5-format file and can be read using ``scipy.io.matlab.loadmat`` in Python. 
-\*space-T1w\*_dwimap.fib.gz,DSI Studio fib format containing the GQI ODFs used for AutoTrack. 
-\*space-T1w\*_mapping.map.gz,Mapping file produced by DSI Studio.
+\*_connectivity.mat,MATLAB format mat file containing connectivity matrices for all the selected atlases. This is an hdf5-format file and can be read using ``scipy.io.matlab.loadmat`` in Python.
+\*space-ACPC\*_dwimap.fib.gz,DSI Studio fib format containing the GQI ODFs used for AutoTrack.
+\*space-ACPC\*_mapping.map.gz,Mapping file produced by DSI Studio.
diff --git a/docs/nonscalars/mrtrix_anat.csv b/docs/nonscalars/mrtrix_anat.csv
index 804d1de2..de0da820 100644
--- a/docs/nonscalars/mrtrix_anat.csv
+++ b/docs/nonscalars/mrtrix_anat.csv
@@ -1,2 +1,2 @@
-\*space-T1w\*seg-hsvs\*_dseg.nii.gz,Hybrid Surface/Volume Segmentation in MRtrix3 5tt format. Aligned in coordinate space to ``space-T1w``. 
+\*space-ACPC\*seg-hsvs\*_dseg.nii.gz,Hybrid Surface/Volume Segmentation in MRtrix3 5tt format. Aligned in coordinate space to ``space-ACPC``.
 \*space-fsnative\*seg-hsvs\*_dseg.nii.gz,Hybrid Surface/Volume Segmentation in MRtrix3 5tt format. Aligned to the FreeSurfer ``orig.mgz`` image.
diff --git a/docs/nonscalars/ss3t_autotrack.csv b/docs/nonscalars/ss3t_autotrack.csv
index 540045f2..7d9c6cdf 100644
--- a/docs/nonscalars/ss3t_autotrack.csv
+++ b/docs/nonscalars/ss3t_autotrack.csv
@@ -1,5 +1,5 @@
-\*_streamlines.tck.gz,One tck.gz per bundle. The bundle represented by this file is specified in the ``bundle-`` tag. 
-\*bundles-DSIStudio\*_scalarstats.csv,Statistics on scalars produced by this workflow 
+\*_streamlines.tck.gz,One tck.gz per bundle. The bundle represented by this file is specified in the ``bundle-`` tag.
+\*bundles-DSIStudio\*_scalarstats.csv,Statistics on scalars produced by this workflow
 \*bundles-DSIStudio\*_tdistats.tsv,Statistics on streamline density in voxels
-\*space-T1w\*_dwimap.fib.gz,DSI Studio fib format containing the SS3T FODs used for AutoTrack. 
-\*space-T1w\*_mapping.map.gz,Mapping file produced by DSI Studio.
+\*space-ACPC\*_dwimap.fib.gz,DSI Studio fib format containing the SS3T FODs used for AutoTrack.
+\*space-ACPC\*_mapping.map.gz,Mapping file produced by DSI Studio.
diff --git a/qsirecon/data/nonscalars/mrtrix_anat.yaml b/qsirecon/data/nonscalars/mrtrix_anat.yaml
index 9d0d8e30..930f1456 100644
--- a/qsirecon/data/nonscalars/mrtrix_anat.yaml
+++ b/qsirecon/data/nonscalars/mrtrix_anat.yaml
@@ -8,7 +8,7 @@ qsiprep_5tt_hsvs:
     metadata:
         Description: |
             Hybrid Surface/Voume Segmentation in MRtrix3 5tt format.
-            Aligned in coordinate space to ``space-T1w``.
+            Aligned in coordinate space to ``space-ACPC``.
 
 fs_5tt_hsvs:
     bids:
diff --git a/qsirecon/interfaces/mrtrix.py b/qsirecon/interfaces/mrtrix.py
index d9cabd78..0742960c 100644
--- a/qsirecon/interfaces/mrtrix.py
+++ b/qsirecon/interfaces/mrtrix.py
@@ -1057,7 +1057,7 @@ def _rename_connectome(connectome_csv, suffix="_connectome.csv"):
     ...    "calc_connectivity/mrtrix_atlasgraph/" \
     ...    "schaefer200x17_sift_invnodevol_radius2_count/connectome.csv"
     >>> _rename_connectome(pth)
-    "sub-X_ses-1_space-T1w_desc-preproc_schaefer200x17_sift_invnodevol_radius2_count_connectome.csv"
+    "sub-X_ses-1_space-ACPC_desc-preproc_schaefer200x17_sift_invnodevol_radius2_count_connectome.csv"
     """
     parts = connectome_csv.split(os.sep)
     conn_name = parts[-2]
diff --git a/qsirecon/interfaces/scalar_mapping.py b/qsirecon/interfaces/scalar_mapping.py
index df8b00f6..ddb3da95 100644
--- a/qsirecon/interfaces/scalar_mapping.py
+++ b/qsirecon/interfaces/scalar_mapping.py
@@ -241,7 +241,10 @@ def _do_mapping(self, runtime):
                 continue
             new_metadata = recon_scalar.copy()
             output_fname = op.split(recon_scalar["path"])[1]
-            output_fname = output_fname.replace("_space-T1w_", "_transformed_")
+            output_fname = output_fname.replace("_space-T1w_", "_transformed_").replace(
+                "_space-ACPC_",
+                "_transformed_",
+            )
             output_fname = op.join(runtime.cwd, output_fname)
             transform = ants.ApplyTransforms(
                 input_image=recon_scalar["path"],
diff --git a/qsirecon/tests/data/mrtrix_multishell_msmt_hsvs_outputs.txt b/qsirecon/tests/data/mrtrix_multishell_msmt_hsvs_outputs.txt
index 6febe13f..daeb0bd9 100644
--- a/qsirecon/tests/data/mrtrix_multishell_msmt_hsvs_outputs.txt
+++ b/qsirecon/tests/data/mrtrix_multishell_msmt_hsvs_outputs.txt
@@ -36,7 +36,7 @@ logs/CITATION.md
 logs/CITATION.tex
 sub-01
 sub-01/anat
-sub-01/anat/sub-01_space-T1w_seg-hsvs_probseg.nii.gz
+sub-01/anat/sub-01_space-ACPC_seg-hsvs_probseg.nii.gz
 sub-01/anat/sub-01_space-fsnative_seg-hsvs_probseg.mif.gz
 sub-01/dwi
 sub-01/dwi/sub-01_dir-AP_rec-downsampled_run-001_space-T1w_seg-AAL116_dseg.mif.gz
diff --git a/qsirecon/workflows/recon/utils.py b/qsirecon/workflows/recon/utils.py
index c4f6c06e..1de9feb4 100644
--- a/qsirecon/workflows/recon/utils.py
+++ b/qsirecon/workflows/recon/utils.py
@@ -55,7 +55,6 @@ def init_discard_repeated_samples_wf(
     inputs_dict,
     name="discard_repeats",
     qsirecon_suffix="",
-    space="T1w",
     params={},
 ):
     """Remove a sample if a similar direction/gradient has already been sampled."""

From c280cb7946f8e97422a4000baea75450579278a0 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 19 Nov 2024 17:08:20 -0500
Subject: [PATCH 3/3] Update builtin_workflows.rst

---
 docs/builtin_workflows.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/builtin_workflows.rst b/docs/builtin_workflows.rst
index 6e0db92e..c213198f 100644
--- a/docs/builtin_workflows.rst
+++ b/docs/builtin_workflows.rst
@@ -585,10 +585,10 @@ associated reconstruction workflows dataset.
          qsirecon-<suffix>/
             sub-<label>/
                dwi/
-                  sub-<label>_space-T1w_seg-<label>_dseg.nii.gz
-                  sub-<label>_space-T1w_seg-<label>_dseg.mif.gz
-                  sub-<label>_space-T1w_seg-<label>_dseg.json
-                  sub-<label>_space-T1w_seg-<label>_dseg.tsv
+                  sub-<label>_space-ACPC_seg-<label>_dseg.nii.gz
+                  sub-<label>_space-ACPC_seg-<label>_dseg.mif.gz
+                  sub-<label>_space-ACPC_seg-<label>_dseg.json
+                  sub-<label>_space-ACPC_seg-<label>_dseg.tsv
 
 
 .. _custom_atlases: