From f53b69a8ff0fc202a7e6ae9016c40acfdcbe9cdd Mon Sep 17 00:00:00 2001
From: Nicholas Alexander <nalexander@fil.ion.ucl.ac.uk>
Date: Mon, 30 Oct 2023 12:57:03 +0000
Subject: [PATCH] Added a few fixes and updated defaults

---
 preprocessing/ft_wrapper_spm_amm.m | 81 ++++++++++++++++++++++++------
 1 file changed, 67 insertions(+), 14 deletions(-)

diff --git a/preprocessing/ft_wrapper_spm_amm.m b/preprocessing/ft_wrapper_spm_amm.m
index 7fa49b5..5dc4de8 100644
--- a/preprocessing/ft_wrapper_spm_amm.m
+++ b/preprocessing/ft_wrapper_spm_amm.m
@@ -5,7 +5,11 @@
 %   cfg.correctgrad         = Correct the forward model ('yes' or no';
 %                             default = 'no'). This is experimental and
 %                             should be used with caution.
-%
+%	cfg.corrLim				= default 1, adjust to 0.98 or 0.9 as necessary.
+%	cfg.li					= internal harmonic order (default = 9)
+%	cfg.le					= external harmonic order (default = 2)
+%	cfg.window				= temporal window size in seconds (default = 10)
+% 
 % Copyright (C) 2023 Wellcome Trust Centre for Neuroimaging
 %
 % Author for this wrapper:      Robert Seymour (rob.seymour@ucl.ac.uk)
@@ -19,8 +23,30 @@
     cfg.correctgrad = 'yes';
 end
 
+if ~isfield(cfg, 'corrLim')
+	cfg.corrLim = 1;
+end
+
+if ~isfield(cfg, 'li')
+	cfg.li = 9;
+end
+
+if ~isfield(cfg, 'le')
+	cfg.le = 2;
+end
+
+if ~isfield(cfg, 'window')
+	cfg.window = 10;
+end
+
 %% Add paths
-addpath('D:\scripts\tim_amm'); % FIXME Hardcoded for Rob at the moment
+% Check if fieldtrip is currently in the path
+try 
+	[~, ftpath] = ft_version;
+	rmpath(ftpath);
+catch
+end
+
 addpath(cfg.path_to_SPM)
 warning('off','all');
 spm('defaults', 'eeg')
@@ -39,12 +65,17 @@
 warning('on','all');
 
 %% AMM
-% FIXME Currently hard-coded
 S               = [];
 S.D             = data_SPM;
-S.le            = 1;
-S.corrLim       = 0.98;
-data_SPM_AMM    = spm_opm_amm(S); % Contact Tim Tierney for these scripts
+S.corrLim       = cfg.corrLim;
+S.li			= cfg.li;
+S.le			= cfg.le;
+S.window		= cfg.window;
+try
+	data_SPM_AMM    = spm_opm_amm(S); % Contact Tim Tierney for these scripts
+catch
+	error('Please check that you have the latest version of SPM which includes spm_opm_amm.');
+end
 
 %% To Fieldtrip
 data_out = data_SPM_AMM.ftraw;
@@ -67,9 +98,6 @@
 warning('off','all');
 rmpath(genpath(cfg.path_to_SPM));
 warning('on','all');
-% disp('Adding Fieldtrip back your path...');
-% addpath(ft_path);
-%ft_defaults
 
 % Delete SPM data
 try
@@ -80,6 +108,18 @@
 catch
 end
 
+
+% Add fieldtrip back
+try
+	addpath(ftpath);
+	ft_defaults;
+catch
+end
+
+
+end
+
+
 % Subfunction to remove sensors from the grad structure not in the data
 function dataout = fixsens(data1)
     chans2keep = ismember(data1.grad.label,data1.label);
@@ -91,7 +131,17 @@
 
     for p = 1:length(pot_grad_fields)
         if isfield(grad_mod,pot_grad_fields{p})
-            eval(['grad_mod.' pot_grad_fields{p} ' = grad_mod.' pot_grad_fields{p} '(chans2keep,:)']);
+            % Define the field name to update
+			fieldName = pot_grad_fields{p};
+			
+			% Check if the field exists in grad_mod
+			if isfield(grad_mod, fieldName)
+    			% Access and update the field directly
+    			grad_mod.(fieldName) = grad_mod.(fieldName)(chans2keep, :);
+			else
+    			% Handle the case when the field does not exist
+    			disp(['Field "', fieldName, '" does not exist in grad_mod.']);
+			end
         end
     end
 
@@ -100,8 +150,13 @@
 
     for p = 1:length(pot_grad_fields)
         if isfield(grad_mod,pot_grad_fields{p})
-            eval(['grad_mod.' pot_grad_fields{p} ...
-                ' = grad_mod.' pot_grad_fields{p} '(chans2keep)']);
+			fieldName = pot_grad_fields{p};
+			
+			if isfield(grad_mod, fieldName)
+    			grad_mod.(fieldName) = grad_mod.(fieldName)(chans2keep);
+			else
+    			disp(['Field "', fieldName, '" does not exist in grad_mod.']);
+			end
         end
     end
 
@@ -114,5 +169,3 @@
     dataout=data1;
     dataout.grad = grad_mod;
 end
-
-end