From 33884d2e5670762a035c3fe3b77e00721157a461 Mon Sep 17 00:00:00 2001
From: Jason Kai <21226986+kaitj@users.noreply.github.com>
Date: Tue, 11 Feb 2025 13:07:33 -0500
Subject: [PATCH] Fix mrtrix3 5ttgen descriptor

- Change all outputs from "File" -> "String"
- Add command-line flag's for thalami and hippocampi arguments in "hsvs"
  algorithm
---
 descriptors/mrtrix/5ttgen.json | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/descriptors/mrtrix/5ttgen.json b/descriptors/mrtrix/5ttgen.json
index b4d6071de..3da3ee59f 100644
--- a/descriptors/mrtrix/5ttgen.json
+++ b/descriptors/mrtrix/5ttgen.json
@@ -35,7 +35,7 @@
               "name": "output",
               "value-key": "[OUTPUT]",
               "description": "The output 5TT image",
-              "type": "File",
+              "type": "String",
               "optional": false
             },
             {
@@ -76,7 +76,7 @@
               "name": "output",
               "value-key": "[OUTPUT]",
               "description": "The output 5TT image",
-              "type": "File",
+              "type": "String",
               "optional": false
             },
             {
@@ -135,7 +135,7 @@
               "name": "output",
               "value-key": "[OUTPUT]",
               "description": "The output 5TT image",
-              "type": "File",
+              "type": "String",
               "optional": false
             }
           ],
@@ -167,7 +167,7 @@
               "name": "output",
               "value-key": "[OUTPUT]",
               "description": "The output 5TT image",
-              "type": "File",
+              "type": "String",
               "optional": false
             },
             {
@@ -182,18 +182,28 @@
             {
               "id": "hippocampi",
               "name": "hippocampi",
+              "command-line-flag": "-hippocampi",
               "value-key": "[OPTIONS_HIPPOCAMPI]",
               "description": "Select method to be used for hippocampi (& amygdalae) segmentation; options are: subfields,first,aseg",
-              "value-choices": ["subfields", "first", "aseg"],
+              "value-choices": [
+                "subfields",
+                "first",
+                "aseg"
+              ],
               "type": "String",
               "optional": true
             },
             {
               "id": "thalami",
               "name": "thalami",
+              "command-line-flag": "-thalami",
               "value-key": "[OPTIONS_THALAMI]",
               "description": "Select method to be used for thalamic segmentation; options are: nuclei,first,aseg",
-              "value-choices": ["nuclei", "first", "aseg"],
+              "value-choices": [
+                "nuclei",
+                "first",
+                "aseg"
+              ],
               "type": "String",
               "optional": true
             },
@@ -362,4 +372,4 @@
     }
   ],
   "url": "https://www.mrtrix.org/"
-}
+}
\ No newline at end of file