[ENH] Change long_id format

clinica/pipelines/anatomical/freesurfer/longitudinal/correction/utils.py

@@ -282,7 +282,7 @@ def get_processed_images(
     atlas: Optional[str] = None,
 ) -> list[str]:
     """
-    Extract image IDs (e.g. ["sub-CLNC01_ses-M000_long-M000M018", "sub-CLNC01_ses-M018_long-M000M018"]) of outputs
+    Extract image IDs (e.g. ["sub-CLNC01_ses-M000_long-M000+M018", "sub-CLNC01_ses-M018_long-M000+M018"]) of outputs
     already processed by T1FreeSurferLongitudinalCorrection pipeline.
     """
     image_ids = []

clinica/pipelines/anatomical/freesurfer/longitudinal/template/pipeline.py

@@ -35,7 +35,7 @@ def get_processed_images(
                 list_participant_id, list_long_id, caps_directory, T1_FS_T_DESTRIEUX
             )
             image_ids = [
-                re.search(r"(sub-[a-zA-Z0-9]+)_(long-[a-zA-Z0-9]+)", file).group()
+                re.search(r"(sub-[a-zA-Z0-9]+)_(long-[a-zA-Z0-9+]+)", file).group()
                 for file in t1_freesurfer_files
             ]
         return image_ids

clinica/pipelines/anatomical/freesurfer/longitudinal/utils.py

@@ -71,7 +71,7 @@ def grab_image_ids_from_caps_directory(
 
     part_ids = ["sub-CLNC01",  "sub-CLNC01",  "sub-CLNC01" ]
     sess_ids = ["ses-M000",     "ses-M018",     "ses-M036"    ]
-    long_ids = ["long-M000M018", "long-M000M018", "long-M000M018"]
+    long_ids = ["long-M000+M018", "long-M000+M018", "long-M000+M018"]
     (sub-CLNC02 does not have longitudinal ID so it does not appear on the result)
 
     Parameters

clinica/utils/longitudinal.py

@@ -26,16 +26,16 @@ def get_long_id(session_ids: List[str]) -> str:
     >>> get_long_id(['ses-M000'])
     'long-M000'
     >>> get_long_id(['ses-M000', 'ses-M018', 'ses-M036'])
-    'long-M000M018M036'
+    'long-M000+M018+M036'
     >>> get_long_id(['ses-M018', 'ses-M036', 'ses-M000'])
-    'long-M000M018M036'
+    'long-M000+M018+M036'
     """
     if not all([session_id.startswith("ses-") for session_id in session_ids]):
         raise ValueError(
             "Expected a list of session IDs of the form ses-XXX, "
             f"but received {session_ids} instead."
         )
-    return "long-" + "".join(
+    return "long-" + "+".join(
         [session_id.lstrip("ses-") for session_id in sorted(session_ids)]
     )
 
@@ -62,7 +62,7 @@ def get_participants_long_id(
     --------
     >>> from clinica.utils.longitudinal import get_participants_long_id
     >>> get_participants_long_id(['sub-CLNC01', 'sub-CLNC01', 'sub-CLNC02'], ['ses-M000', 'ses-M018', 'ses-M000'])
-    ['long-M000M018', 'long-M000M018', 'long-M000']
+    ['long-M000+M018', 'long-M000+M018', 'long-M000']
     """
     from .participant import get_unique_subjects
 

docs/CAPS/Introduction.md

@@ -34,7 +34,7 @@ You will find this notion when working on longitudinal datasets.
 This is simply a label that will define the set of sessions considered.
 Unlike group, longitudinal template is dedicated to intra-subject analysis.
 Besides, the longitudinal label for a participant is defined concatenating the different session labels in alphabetical order so that the longitudinal label will be unique.
-For instance, if the intra-subject template is computed on `M018` and `M000` sessions, the longitudinal ID will be `long-M000M018`.
+For instance, if the intra-subject template is computed on `M018` and `M000` sessions, the longitudinal ID will be `long-M000+M018`.
 
 ## Differences with BIDS
 
@@ -123,19 +123,19 @@ groups/
 
 This CAPS folder contains the outputs of longitudinal segmentations performed with [FreeSurfer](../Software/Third-party.md#freesurfer) for a fictional participant `CLNC01` at sessions `M000` and `M018`.
 First, the [`t1-freesurfer` pipeline](../Pipelines/T1_FreeSurfer.md) is run on the two sessions.
-Then, the [`t1-freesurfer-longitudinal` pipeline](../Pipelines/T1_FreeSurfer_Longitudinal.md) will compute the intra-subject template `sub-CLNC01_long-M000M018` using the `M000` and `M018` sessions.
-This template is finally used to longitudinally correct the segmentations, whose results are stored in the `sub-CLNC01_ses-M000.long.sub-CLNC01_long-M000M018` and `sub-CLNC01_ses-M018.long.sub-CLNC01_long-M000M018` folders.
+Then, the [`t1-freesurfer-longitudinal` pipeline](../Pipelines/T1_FreeSurfer_Longitudinal.md) will compute the intra-subject template `sub-CLNC01_long-M000+M018` using the `M000` and `M018` sessions.
+This template is finally used to longitudinally correct the segmentations, whose results are stored in the `sub-CLNC01_ses-M000.long.sub-CLNC01_long-M000+M018` and `sub-CLNC01_ses-M018.long.sub-CLNC01_long-M000+M018` folders.
 
 Of note, the `<time_point_id>.long.<template_id>` naming comes from [FreeSurfer](../Software/Third-party.md#freesurfer) when running the longitudinal `recon-all` command.
 
 ```Text
 dataset_description.json
 subjects/
 ├── sub-CLNC01/
-│   ├── long-M000M018/
-│   │   ├── long-M000M018_sessions.tsv
+│   ├── long-M000+M018/
+│   │   ├── long-M000+M018_sessions.tsv
 │   │   └── freesurfer_unbiased_template/
-│   │       └── sub-CLNC01_long-M000M018/
+│   │       └── sub-CLNC01_long-M000+M018/
 │   │           ├── base-tps/
 │   │           ├── label/
 │   │           ├── mri/
@@ -150,10 +150,10 @@ subjects/
 │   │       │       ├── mri/
 │   │       │       ├── stats/
 │   │       │       └── surf/
-│   │       └── long-M000M018/
+│   │       └── long-M000+M018/
 │   │           └── freesurfer_longitudinal/
 │   │               ├── regional_measures/
-│   │               └── sub-CLNC01_ses-M000.long.sub-CLNC01_long-M000M018/
+│   │               └── sub-CLNC01_ses-M000.long.sub-CLNC01_long-M000+M018/
 │   │                   ├── label/
 │   │                   ├── mri/
 │   │                   ├── stats/
@@ -167,10 +167,10 @@ subjects/
 │           │       ├── mri/
 │           │       ├── stats/
 │           │       └── surf/
-│           └── long-M000M018
+│           └── long-M000+M018
 │               └── freesurfer_longitudinal
 │                   ├── regional_measures
-│                   └── sub-CLNC01_ses-M018.long.sub-CLNC01_long-M000M018/
+│                   └── sub-CLNC01_ses-M018.long.sub-CLNC01_long-M000+M018/
 │                       ├── label/
 │                       ├── mri/
 │                       ├── stats/

docs/Pipelines/T1_FreeSurfer_Longitudinal.md

@@ -106,7 +106,7 @@ Results stored in the following folder of the
 [CAPS hierarchy](../../CAPS/Specifications/#t1-freesurfer-longitudinal-freesurfer-based-longitudinal-processing-of-t1-weighted-mr-images):
 `subjects/<participant_id>/<long_id>/freesurfer_unbiased_template/<participant_id>_<long_id>`.
 
-`<long_label>` is an identifier defined by concatenating all the sessions associated with the current `<participant_id>` (e.g. if the template for participant `sub-CLNC01` is built from sessions `M00`, `M01`, `M05`, then `<long_label>` will be `M00M01M05`).
+`<long_label>` is an identifier defined by concatenating all the sessions associated with the current `<participant_id>` (e.g. if the template for participant `sub-CLNC01` is built from sessions `M00`, `M01`, `M05`, then `<long_label>` will be `M00+M01+M05`).
 See [CAPS specifications](../../CAPS/Introduction/#subject-and-group-naming) for full definition and example of `<long_id>`.
 
 This folder contains the standard output structure of the `recon-all` command (`label/`, `mri/`, `surf/`, etc.) already explained in the [`t1-freesurfer`](../T1_FreeSurfer) pipeline.

test/unittests/utils/test_longitudinal.py

@@ -5,9 +5,9 @@
     "session_ids,expected",
     [
         (["ses-M000"], "long-M000"),
-        (["ses-M000", "ses-M018", "ses-M036"], "long-M000M018M036"),
-        (["ses-M018", "ses-M036", "ses-M000"], "long-M000M018M036"),
-        (["ses-foo", "ses-bar", "ses-baz", "ses-foobar"], "long-barbazfoofoobar"),
+        (["ses-M000", "ses-M018", "ses-M036"], "long-M000+M018+M036"),
+        (["ses-M018", "ses-M036", "ses-M000"], "long-M000+M018+M036"),
+        (["ses-foo", "ses-bar", "ses-baz", "ses-foobar"], "long-bar+baz+foo+foobar"),
     ],
 )
 def test_get_long_id(session_ids, expected):
@@ -40,7 +40,7 @@ def test_get_long_id_errors(session_ids):
         (
             ["sub-CLNC01", "sub-CLNC01", "sub-CLNC02"],
             ["ses-M000", "ses-M018", "ses-M000"],
-            ["long-M000M018", "long-M000M018", "long-M000"],
+            ["long-M000+M018", "long-M000+M018", "long-M000"],
         )
     ],
 )
@@ -64,8 +64,8 @@ def test_save_long_id(tmp_path):
 
     save_long_id(["ses-M000", "ses-M018", "ses-M036"], output_dir)
 
-    assert (output_dir / "long-M000M018M036_sessions.tsv").exists()
-    saved_ids = (output_dir / "long-M000M018M036_sessions.tsv").read_text()
+    assert (output_dir / "long-M000+M018+M036_sessions.tsv").exists()
+    saved_ids = (output_dir / "long-M000+M018+M036_sessions.tsv").read_text()
     assert saved_ids == "session_id\nses-M000\nses-M018\nses-M036\n"