From 52f8e9ca3e313ae98a23b51ea2b9df60bf9e66d8 Mon Sep 17 00:00:00 2001
From: Robert <52195853+robdahn@users.noreply.github.com>
Date: Fri, 7 Jun 2024 14:40:04 +0200
Subject: [PATCH] Added surface ROI in expert GUI

(Re)added surface ROI output GUI setting for experts.
---
 cat_conf_output.m | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/cat_conf_output.m b/cat_conf_output.m
index 25ad12bd..7fa12f76 100644
--- a/cat_conf_output.m
+++ b/cat_conf_output.m
@@ -454,7 +454,12 @@
   output      = cfg_branch;
   output.tag  = 'output';
   output.name = 'Writing options';
-  output.val  = {BIDS surface surf_measures ROI grey white csf gmt pp wmh sl tpmc atlas label labelnative bias las jacobianwarped warps rmat}; 
+  if expert
+    output.val  = {BIDS surface surf_measures ROI sROI grey white csf gmt pp wmh sl tpmc atlas label labelnative bias las jacobianwarped warps rmat}; 
+  else
+    output.val  = {BIDS surface surf_measures ROI grey white csf gmt pp wmh sl tpmc atlas label labelnative bias las jacobianwarped warps rmat}; 
+  end
+    
   output.help = {
   'There are a number of options about what kind of data you like save. The routine can be used for saving images of tissue classes, as well as bias corrected images. The native space option will save a tissue class image (p*) that is in alignment with the original image. You can also save spatially normalised versions - both with (m[0]wp*) and without (wp*) modulation. In the cat toolbox, the voxel size of the spatially normalised versions is 1.5 x 1.5 x 1.5mm as default. The saved images of the tissue classes can directly be used for doing voxel-based morphometry (both un-modulated and modulated). All you need to do is smooth them and do the stats (which means no more questions on the mailing list about how to do "optimized VBM"). Please note that many less-common options are only available in expert mode (e.g. CSF, labels, atlas maps).'
   ''