From 6586245471a60361c07d93f61497939d2d3bb57f Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Thu, 27 Nov 2025 21:50:06 -0500
Subject: [PATCH] update config

---
 config/config_cogms.yml | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/config/config_cogms.yml b/config/config_cogms.yml
index 1e49615..2f35b88 100644
--- a/config/config_cogms.yml
+++ b/config/config_cogms.yml
@@ -95,44 +95,52 @@ post_convert_fixes:
   - name: remove_rois
     pattern: "anat/*ROI1.*"
     action: remove
-  - name: add_num_shots_sa2rage
+
+  - name: remove_scans_tsv
+    pattern: "*scans.tsv"
+    action: remove
+
+  - name: sa2rage_metadata
     pattern: "fmap/*TB1SRGE.json"
     action: update_json
     updates:
-      NumberShots: "placeholder"
-  - name: add_num_shots_mp2rage
+      NumberShots: 1
+      RepetitionTimeExcitation: 0.002
+      RepetitionTimePreparation: 2.4
+
+  - name: mp2rage_metadata
     pattern: "anat/*inv-*MP2RAGE.json"
     action: update_json
     updates:
-      NumberShots: "placeholder"
+      NumberShots: 1  # Single-shot
+      RepetitionTimeExcitation: 0.0079 # Echo spacing from the protocol pdf
+      RepetitionTimePreparation: 6 
+
   - name: phase_units
     pattern: "*/*part-phase*.json"
     action: update_json
     updates:
       Units: rad
+
   - name: phase_units_
     pattern: "*/*phase.json"
     action: update_json
     updates:
       Units: rad
+
   - name: remove_dupe_t1maps
     pattern: "*/*run-*_*T1map.nii.gz"
     action: remove_duplicate_niftis
+
   - name: remove_dupe_t1w
     pattern: "*/*run-*_*T1w.nii.gz"
     action: remove_duplicate_niftis
+
   - name: remove_dupe_mp2rage
     pattern: "*/*run-*_*MP2RAGE.nii.gz"
     action: remove_duplicate_niftis
 
 
-
-
-
-
-
-
-
 bidsignore:
   - '*_acq-b1Div_*'
   - '*_b1DivImg.*'