From e3d79bd607f74b9ec3f824786738e28f35c485c1 Mon Sep 17 00:00:00 2001
From: Jeff Stout <stoutjd@nih.gov>
Date: Tue, 15 Oct 2024 22:31:41 -0400
Subject: [PATCH] ENH - piped in freesurfer sbatch job submission to gui

---
 nih2mne/GUI/qt_gui.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/nih2mne/GUI/qt_gui.py b/nih2mne/GUI/qt_gui.py
index 60fd6c7..79a199d 100644
--- a/nih2mne/GUI/qt_gui.py
+++ b/nih2mne/GUI/qt_gui.py
@@ -346,7 +346,13 @@ def select_qa_file(self):
         
     
     def proc_freesurfer(self):
-        self.bids_project.run_anat_pipeline()   
+        'Loop over subjects that do not have a fs dir and run fs'
+        issues = self.bids_project.issues
+        freesurfer_proclist=[] 
+        for subject, bids_info in self.bids_project.subjects.items():
+            if subject in issues['Freesurfer_notStarted']:
+                print(f'Submitting sbatch job for {subject}')
+                bids_info.proc_freesurfer()
     
     
     def proc_mriprep(self):