Merge pull request #24 from fliem/long

fixes behav in singl-session-subjects in long study

Author: chrisgorgo

circle.yml

@@ -27,7 +27,7 @@ test:
   override:
     # print version
     - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset bids/${CIRCLE_PROJECT_REPONAME,,} --version
-    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --stages autorecon1:
+    - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/outputs1:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01 --license_key="~/test.key" --stages autorecon1 && cat ${HOME}/outputs1/sub-01/scripts/recon-all.done :
         timeout: 21600
     # group2 tests
     - docker run -ti --rm --read-only -v /tmp:/tmp -v /var/tmp:/var/tmp -v ${HOME}/data/ds114_test1:/bids_dataset -v ${HOME}/data/ds114_test1_freesurfer:/outputs bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group2 --license_key="~/test.key"  && mkdir -p ${HOME}/outputs1/ && sudo mv ${HOME}/data/ds114_test1_freesurfer/00_group* ${HOME}/outputs1/ && cat ${HOME}/outputs1/00_group2_stats_tables/lh.aparc.thickness.tsv :

run.py

@@ -89,17 +89,41 @@ def run(command, env={}, ignore_errors=False):
 run("bids-validator " + args.bids_dir)
 
 subject_dirs = glob(os.path.join(args.bids_dir, "sub-*"))
+
 if args.acquisition_label:
     acq_tpl = "*acq-%s*" % args.acquisition_label
 else:
     acq_tpl = "*"
 
+# if there are session folders, check if study is truly longitudinal by
+# searching for the first subject with more than one valid sessions
+multi_session_study = False
+if glob(os.path.join(args.bids_dir, "sub-*", "ses-*")):
+    subjects = [subject_dir.split("-")[-1] for subject_dir in subject_dirs]
+    for subject_label in subjects:
+        session_dirs = glob(os.path.join(args.bids_dir,"sub-%s"%subject_label,"ses-*"))
+        sessions = [os.path.split(dr)[-1].split("-")[-1] for dr in session_dirs]
+        n_valid_sessions = 0
+        for session_label in sessions:
+            if glob(os.path.join(args.bids_dir, "sub-%s"%subject_label,
+                                                "ses-%s"%session_label,
+                                                "anat",
+                                                "%s_T1w.nii*"%acq_tpl)):
+                n_valid_sessions += 1
+        if n_valid_sessions > 1:
+            multi_session_study = True
+            break
+
+if multi_session_study and (args.multiple_sessions == "longitudinal"):
+    longitudinal_study = True
+else:
+    longitudinal_study = False
+
 if args.refine_pial_acquisition_label:
     acq_t2 = "*acq-%s*" % args.refine_pial_acquisition_label
 else:
     acq_t2 = "*"
 
-
 subjects_to_analyze = []
 # only for a subset of subjects
 if args.participant_label:
@@ -125,23 +149,10 @@ def run(command, env={}, ignore_errors=False):
             ignore_errors=True)
 
     for subject_label in subjects_to_analyze:
-
-        # Check for multiple sessions to combine as a multiday session or as a longitudinal stream
         session_dirs = glob(os.path.join(args.bids_dir,"sub-%s"%subject_label,"ses-*"))
         sessions = [os.path.split(dr)[-1].split("-")[-1] for dr in session_dirs]
-        longitudinal_study = False
-        n_valid_sessions = 0
-        for session_label in sessions:
-            if glob(os.path.join(args.bids_dir, "sub-%s"%subject_label,
-                                                "ses-%s"%session_label,
-                                                "anat",
-                                                "%s_T1w.nii*"%acq_tpl)):
-                n_valid_sessions += 1
-        if n_valid_sessions > 1 and args.multiple_sessions == "longitudinal":
-            longitudinal_study = True
 
         timepoints = []
-
         if len(sessions) > 0 and longitudinal_study == True:
             # Running each session separately, prior to doing longitudinal pipeline
             for session_label in sessions: