From 2e1d5ee2e2ee4188fbe873a03a34172a3348ad1e Mon Sep 17 00:00:00 2001
From: Tristan Kuehn <tkuehn@uwo.ca>
Date: Wed, 20 Sep 2023 14:23:13 -0400
Subject: [PATCH 1/3] Make output_type a tuple

This is a bug that heudiconv used to silently fix but doesn't anymore,
so it causes problem with new versions of heudiconv.
---
 heuristics/cfmm_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/heuristics/cfmm_base.py b/heuristics/cfmm_base.py
index 4e9c0a6..18fa643 100644
--- a/heuristics/cfmm_base.py
+++ b/heuristics/cfmm_base.py
@@ -1,6 +1,6 @@
 import os
 
-def create_key(template, outtype=('nii.gz'), annotation_classes=None):
+def create_key(template, outtype=('nii.gz',), annotation_classes=None):
     if template is None or not template:
         raise ValueError('Template must be a valid format string')
     return (template, outtype, annotation_classes)

From a31df91efbff2896fa3c8184c08d9c01925e8cdb Mon Sep 17 00:00:00 2001
From: Tristan Kuehn <tkuehn@uwo.ca>
Date: Wed, 20 Sep 2023 14:25:57 -0400
Subject: [PATCH 2/3] Update heudiconv and dcm2niix

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 52a6d6a..5bbf3a6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,10 +2,10 @@ FROM debian:bullseye
 LABEL maintainer="<alik@robarts.ca>"
 
 # dcm2niix version
-ENV DCM2NIIXTAG v1.0.20220720
+ENV DCM2NIIXTAG v1.0.20230411
 
 #heudiconv version:
-ENV HEUDICONVTAG v0.11.3
+ENV HEUDICONVTAG v0.13.1
 
 #bids validator version:
 ENV BIDSTAG 1.9.7

From e681c0b181e551fff496f0de5ecd2d2ed7b81259 Mon Sep 17 00:00:00 2001
From: Tristan Kuehn <tkuehn@uwo.ca>
Date: Wed, 20 Sep 2023 14:26:09 -0400
Subject: [PATCH 3/3] Handle datatype when deleting _ROI files

---
 tar2bids | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tar2bids b/tar2bids
index 58ddc30..a671c6c 100755
--- a/tar2bids
+++ b/tar2bids
@@ -499,7 +499,7 @@ else
 fi
 
 echo "  Removing _ROI#.nii.gz files (unused scale bars from qMRI)..."
-rm -vf $output_dir/sub*/*/*ROI[0-9].nii.gz $output_dir/sub*/ses*/*ROI[0-9].nii.gz 2> /dev/null
+rm -vf $output_dir/sub*/*/*ROI[0-9].nii.gz $output_dir/sub*/ses*/*/*ROI[0-9].nii.gz 2> /dev/null
 
 echo "  Running bids-validator..."
 bids-validator $output_dir | tee  $validator_out