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PHysIO #180 #166: Removing fieldtrip paths instead of spm #181

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PHysIO #180 #166: Removing fieldtrip paths instead of spm #181

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f388e74
Removing fieldtrip folders instead of spm
Apr 11, 2022
4d34fba
Added name to agreement
Apr 11, 2022
26d8b12
Using tapas_pysio_log instead of raising error
Apr 11, 2022
72cd0c2
Moved paths removal to separate function
Apr 12, 2022
c5de309
Added few comments
Apr 12, 2022
c29962d
Moved fieldtrip check to separate file
May 3, 2022
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3 changes: 3 additions & 0 deletions PhysIO/code/readin/tapas_physio_read_physlogfiles.m
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,9 @@
case 'siemens_hcp'
[c, r, t, cpulse, acq_codes, verbose] = ...
tapas_physio_read_physlogfiles_siemens_hcp(log_files, cardiac_modality, verbose);
otherwise
error('Invalid vendor "%s". See tapas_physio_new for supported vendors',...
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log_files.vendor);
end

% Do not prepend for Siemens Tics, since can be as long as a day
Expand Down
29 changes: 18 additions & 11 deletions PhysIO/code/tapas_physio_main_create_regressors.m
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Original file line number Diff line number Diff line change
Expand Up @@ -53,18 +53,19 @@
%% 0. Set Default parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Remove SPM subfolders from path to avoid conflicts with Matlab in-built
% functions used in PhysIO
doCorrectPath = true;
tapas_physio_check_spm(doCorrectPath);
% Silently check proper Batch Editor integration, if SPM exists,
% but don't complain, if there is no SPM installed
isVerbose = false;
tapas_physio_check_spm_batch_editor_integration(isVerbose);
oldPath = path();

% Include subfolders of code to path as well
pathThis = fileparts(mfilename('fullpath'));
addpath(genpath(pathThis));
ft_paths = which('ft_defaults', '-all')
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try
for p = 1:size(ft_paths, 1)
to_remove = fileparts(ft_paths{p});
warning('off', 'MATLAB:rmpath:DirNotFound')
rmpath(genpath(to_remove));
warning('on', 'MATLAB:rmpath:DirNotFound')
end
ft_paths = which('ft_defaults', '-all')

% These parameters could become toolbox inputs...
minConstantIntervalAlertSeconds = 0.2;
Expand Down Expand Up @@ -448,6 +449,12 @@

[physio.verbose] = tapas_physio_print_figs_to_file(physio.verbose);

catch ME
path(oldPath);
rethrow(ME);
end
path(oldPath);

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand All @@ -459,4 +466,4 @@
R = [R, regressors];
names = [names, repmat({name}, 1, size(regressors, 2))];

end
end