From 23919d6043856a0577ae1f53eda44f16eb1e35b4 Mon Sep 17 00:00:00 2001
From: Dawn Smith <dawn.smith@camh.ca>
Date: Mon, 7 Nov 2022 19:57:10 -0500
Subject: [PATCH 1/2] [FIX] Add flag to ignore invalid 'exclude' flag

---
 ciftify/bidsapp/fmriprep_ciftify.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ciftify/bidsapp/fmriprep_ciftify.py b/ciftify/bidsapp/fmriprep_ciftify.py
index fac190c..2f1448a 100755
--- a/ciftify/bidsapp/fmriprep_ciftify.py
+++ b/ciftify/bidsapp/fmriprep_ciftify.py
@@ -154,7 +154,7 @@ def __get_bids_layout(self):
         '''run the BIDS validator and produce the bids_layout'''
         run("bids-validator {}".format(self.bids_dir),  dryrun = DRYRUN)
         try:
-            layout = BIDSLayout(self.bids_dir, exclude=['derivatives'])
+            layout = BIDSLayout(self.bids_dir, invalid_filters='allow', exclude=['derivatives'])
         except:
             logger.critical('Could not parse <bids_dir> {}'.format(self.bids_dir))
             sys.exit(1)

From 52c856dd0471edba49fc3daebc32b6af5055be40 Mon Sep 17 00:00:00 2001
From: Dawn Smith <dawn.smith@camh.ca>
Date: Mon, 7 Nov 2022 19:57:53 -0500
Subject: [PATCH 2/2] [FIX] Remove unneeded pluralization from 'extension' flag

---
 ciftify/bidsapp/fmriprep_ciftify.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ciftify/bidsapp/fmriprep_ciftify.py b/ciftify/bidsapp/fmriprep_ciftify.py
index 2f1448a..3d90848 100755
--- a/ciftify/bidsapp/fmriprep_ciftify.py
+++ b/ciftify/bidsapp/fmriprep_ciftify.py
@@ -350,7 +350,7 @@ def find_participant_bold_inputs(participant_label, settings):
                                        suffix="bold",
                                        session = settings.sessions if len(settings.sessions) > 0 else None,
                                        task = settings.tasks,
-                                       extensions=["nii.gz", "nii"])
+                                       extension=["nii.gz", "nii"])
 
     return bolds
 
@@ -381,7 +381,7 @@ def find_bold_preprocs(bold_input, settings):
                 space = "T1w",
                 suffix = 'preproc',
                 datatype = 'func',
-                extensions = ['.nii.gz', ".nii"])
+                extension = ['.nii.gz', ".nii"])
         return bold_preprocs
 
     #use bids derivatives layout to find the proproc files
@@ -395,7 +395,7 @@ def find_bold_preprocs(bold_input, settings):
                desc = settings.preproc_desc,
                suffix = "bold",
                space = "T1w",
-               extensions=["nii.gz", "nii"])
+               extension=["nii.gz", "nii"])
     return bold_preprocs
 
         ## now need to verify that there is only one...