From b6efbbd8e904bc83f1982380793c6dbfa4ea7db3 Mon Sep 17 00:00:00 2001
From: "Katherine L. Bottenhorn" <kbott006@fiu.edu>
Date: Fri, 14 Jun 2024 15:40:03 -0700
Subject: [PATCH] added some to-dos need to rerun checks

---
 idconn/connectivity.py | 2 ++
 idconn/io.py           | 9 ++++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/idconn/connectivity.py b/idconn/connectivity.py
index 1e79998..5ac1ae2 100644
--- a/idconn/connectivity.py
+++ b/idconn/connectivity.py
@@ -254,6 +254,8 @@ def task_connectivity(
 def rest_connectivity(
     layout, subject, session, task, atlas, confounds=None, connectivity_metric="correlation"
 ):
+    ###################################################################################
+    ################# Needs an option to keep runs separate. ##########################
     """
     Makes connectivity matrices per subject per session per task per condition.
     Parameters
diff --git a/idconn/io.py b/idconn/io.py
index 23b563c..3e1bca9 100644
--- a/idconn/io.py
+++ b/idconn/io.py
@@ -253,6 +253,8 @@ def read_corrmats(layout, task, deriv_name, atlas, z_score=True, vectorized=True
     """Returns a node x node x (subject x session) matrix of correlation matrices
     from a BIDS derivative folder. Optionally returns a node^2 x (subject x session)
     array of vectorized upper triangles of those correlation matrices.
+
+    ME @ ME: NEEDS AN OPTION TO KEEP RUNS SEPARATE. CURRENTLY IT AVERAGES CONFOUNDS AND 
     Parameters
     ----------
     layout : BIDSLayout or str
@@ -356,7 +358,7 @@ def read_corrmats(layout, task, deriv_name, atlas, z_score=True, vectorized=True
                         )
                         # print(confound_means)
             else:
-                path = path = layout.get(
+                path = layout.get(
                     return_type="filename",
                     session=session,
                     desc="confounds",
@@ -397,7 +399,12 @@ def read_corrmats(layout, task, deriv_name, atlas, z_score=True, vectorized=True
                 pass
             if type(path) == list:
                 # print(len(path))
+                ################################################################
+                ############ EEEEEEEEEEEEEEEEEK ################################
+                ############### DOES THIS ONLY GRAB ONE RUN?!?!?! ##############
+                ################################################################
                 path = path[0]
+                
             else:
                 pass
             assert exists(path), f"Corrmat file not found at {path}"