From 789ab96338e96fe2f6a28397fa5a8e335c03ec70 Mon Sep 17 00:00:00 2001
From: ppoulin <ppoulin91@gmail.com>
Date: Fri, 27 May 2022 09:35:05 -0400
Subject: [PATCH] Remove bundle suffix in Fixel_AFD process - Bundle suffix was
 not removed in Fixel_AFD, leading to AFD output filenames with the suffix,
 (e.g. "UF_R_m_cleaned_afd_metric.nii.gz"). Consequently, the following
 processes cannot match bundle names between .trk files and afd Nifti files.
 For example, "Bundle_Endpoints_Metrics" computes the cross product of all
 bundles with all bundle_afd_metrics instead of matching each bundle with its
 afd metric.

---
 main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/main.nf b/main.nf
index c57af22..9a47d4e 100644
--- a/main.nf
+++ b/main.nf
@@ -114,6 +114,7 @@ process Fixel_AFD {
         else
             bname=\$(basename \$bundle .trk)
         fi
+        bname=\${bname/$params.bundle_suffix_to_remove/}
         scil_compute_mean_fixel_afd_from_bundles.py \$bundle $fodf \${bname}_afd_metric.nii.gz
     done
     """