Merge pull request #9 from PennLINC/enh/ukb

session-wise anatomicals for UKB
PennLINC · Nov 18, 2024 · 28a7bb6 · 28a7bb6
2 parents 0abf2c9 + 1337a7e
commit 28a7bb6
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/ingress2qsirecon/utils/functions.py b/ingress2qsirecon/utils/functions.py
@@ -159,32 +159,32 @@ def make_bids_file_paths(subject_layout: dict) -> dict:
             t1_oblique_string = ""
 
         bids_t1w_brain = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + t1_oblique_string + "_desc-preproc_T1w.nii.gz"
+            bids_base_session, "anat", sub_session_string + t1_oblique_string + "_desc-preproc_T1w.nii.gz"
         )
         bids_file_paths.update({"bids_t1w_brain": Path(bids_t1w_brain)})
     if "brain_mask" in subject_layout:
         bids_brain_mask = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + t1_oblique_string + "_desc-brain_mask.nii.gz"
+            bids_base_session, "anat", sub_session_string + t1_oblique_string + "_desc-brain_mask.nii.gz"
         )
         bids_file_paths.update({"bids_brain_mask": Path(bids_brain_mask)})
     if "subject2MNI" in subject_layout:
         bids_subject2MNI = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + f"_from-T1w_to-{mni_template}_mode-image_xfm.h5"
+            bids_base_session, "anat", sub_session_string + f"_from-T1w_to-{mni_template}_mode-image_xfm.h5"
         )
         bids_file_paths.update({"bids_subject2MNI": Path(bids_subject2MNI)})
     else:
         bids_subject2MNI = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + f"_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"
+            bids_base_session, "anat", sub_session_string + f"_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"
         )
         bids_file_paths.update({"bids_subject2MNI": Path(bids_subject2MNI)})
     if "MNI2subject" in subject_layout:
         bids_MNI2subject = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + f"_from-{mni_template}_to-T1w_mode-image_xfm.h5"
+            bids_base_session, "anat", sub_session_string + f"_from-{mni_template}_to-T1w_mode-image_xfm.h5"
         )
         bids_file_paths.update({"bids_MNI2subject": Path(bids_MNI2subject)})
     else:
         bids_MNI2subject = os.path.join(
-            bids_base, "anat", f"sub-{subject}" + f"_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5"
+            bids_base_session, "anat", sub_session_string + f"_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5"
         )
         bids_file_paths.update({"bids_MNI2subject": Path(bids_MNI2subject)})
 

diff --git a/ingress2qsirecon/utils/workflows.py b/ingress2qsirecon/utils/workflows.py
@@ -78,13 +78,13 @@ def create_single_subject_wf(subject_layout, input_pipeline, skip_mni2009c_norm=
 
     # Make BIDS subject output folder
     bids_base = subject_layout['bids_base']
-    if not os.path.exists(bids_base):
-        os.makedirs(Path(bids_base / "anat").resolve(), exist_ok=True)
     session = subject_layout['session']
     if session == None:
         os.makedirs(Path(bids_base / "dwi").resolve(), exist_ok=True)
+        os.makedirs(Path(bids_base / "anat").resolve(), exist_ok=True)
     else:
         os.makedirs(Path(bids_base / f"ses-{session}" / "dwi").resolve(), exist_ok=True)
+        os.makedirs(Path(bids_base / f"ses-{session}" / "anat").resolve(), exist_ok=True)
 
     # Create single subject workflow
     wf_name = f"ingress2qsirecon_single_subject_{subject_name}_wf"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "Ingress2QSIRecon"
-version = "0.2.2"
+version = "0.2.3"
 description = "Tool to ingress data from other pipelines for use in QSIRecon"
 authors = ["Steven Meisler <[email protected]>"]
 readme = "README.md"