-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added a few fixes and updated defaults
- Loading branch information
Nicholas Alexander
committed
Oct 30, 2023
1 parent
63620b3
commit f53b69a
Showing
1 changed file
with
67 additions
and
14 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -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 ([email protected]) | ||
|
@@ -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 |