From 722df81e860ef076a9a6f77c045b53273378bd32 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Yasser=20Alem=C3=A1n=20G=C3=B3mez?= <yasseraleman@yahoo.com>
Date: Tue, 9 Jul 2024 17:04:46 +0200
Subject: [PATCH] Updating the configuration files

---
 config/pipe_config.json             |  7 ++++++-
 config/supraregions_dictionary.json | 12 ++++++------
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/config/pipe_config.json b/config/pipe_config.json
index 5b37292..7c07110 100644
--- a/config/pipe_config.json
+++ b/config/pipe_config.json
@@ -26,7 +26,7 @@
                 "container": "local"
             }
         },
-        "templates": 
+    "templates": 
         {
             "annots": 
             {
@@ -46,5 +46,10 @@
                 "space": "MNI152NLin2009cAsym",
                 "folder": "vol_atlases"
             }
+        },
+    "outputs":
+        {
+            "transforms": "ants-transf2mni",
+            "freesurfer": "freesurfer"
         }
 }
diff --git a/config/supraregions_dictionary.json b/config/supraregions_dictionary.json
index 3cbb921..2f481fd 100644
--- a/config/supraregions_dictionary.json
+++ b/config/supraregions_dictionary.json
@@ -200,7 +200,7 @@
                   "name":"FSThalParc",
                   "description":"# 3. Thalamic parcellation (I): Thalamic parcellation.",
                   "citation":"(Iglesias et al, 2018)",
-                  "source": "freesurfer",
+                  "source": "freesurferextra",
                   "reference":"conform",
                   "type":"custom",
                   "deriv_volfold":"freesurfer-thalamicparc"},
@@ -238,7 +238,7 @@
                   "name":"FSAmygHippoParc",
                   "description":"# 4. Amygdala parcellation (I): Amygdala nuclei parcellation.",
                   "citation":"(Saygin et al, 2017)",
-                  "source": "freesurfer",
+                  "source": "freesurferextra",
                   "reference":"conform",
                   "type":"custom",
                   "deriv_volfold":"freesurfer-amyghippsubfieldsparc"},
@@ -267,7 +267,7 @@
                   "name":"FSAmygHippoParc",
                   "description":"# 5. Hippocampus parcellation (I): Hippocampus subfields parcellation.",
                   "citation":"(Iglesias et al, 2015)",
-                  "source": "freesurfer",
+                  "source": "freesurferextra",
                   "reference":"conform",
                   "type":"custom",
                   "deriv_volfold":"freesurfer-amyghippsubfieldsparc"},
@@ -305,7 +305,7 @@
                   "name":"FSHypoThalParc",
                   "description":"# 6. Hypothalamus parcellation (I): Hypothalamus parcellation.",
                   "citation":"(Billot et al, 2020)",
-                  "source": "freesurfer",
+                  "source": "freesurferextra",
                   "reference":"conform",
                   "type":"custom",
                   "deriv_volfold":"freesurfer-hypothalmicparc"}
@@ -328,7 +328,7 @@
                   "source": "fsl",
                   "reference":"MNI152NLin2009cAsym",
                   "type":"spam",
-                  "deriv_volfold":"freesurfer"},
+                  "deriv_volfold":"abased-suitcerebellum"},
 
             "F": {"atlas":"Aseg",
                   "name":"Aseg",
@@ -345,7 +345,7 @@
                   "name":"Aseg",
                   "description":"# 8. Brainstem parcellation (F): Brainstem parcellation.",
                   "citation":"(Fischl et al, 2002)",
-                  "source": "freesurfer",
+                  "source": "freesurferextra",
                   "reference":"conform",
                   "type":"custom",
                   "deriv_volfold":"freesurfer"},