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[Feature Request] - Defacing of structural images - OspreyCoreg/Seg -… #552

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merged 1 commit into from
Feb 1, 2023
Merged

[Feature Request] - Defacing of structural images - OspreyCoreg/Seg -… #552

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11 changes: 11 additions & 0 deletions coreg/OspreyCoreg.m
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Expand Up @@ -192,6 +192,17 @@
end
end

if MRSCont.opts.img.deface
[anaon_vol_image] = spm_deface({vol_image.fname});
saveDestinationAnon = fullfile(MRSCont.outputFolder, 'DefacedNII'); %CWDJ - Address in future update
if ~exist(saveDestinationAnon,'dir')
mkdir(saveDestinationAnon);
end
[~,AnonName,AnonExt] = fileparts(anaon_vol_image{1});
[~] = movefile(anaon_vol_image{1}, fullfile(saveDestinationAnon,[AnonName AnonExt]));
vol_image = spm_vol(fullfile(saveDestinationAnon,[AnonName AnonExt]));
end

% Save back the image and voxel mask volumes to MRSCont
MRSCont.coreg.vol_image{kk} = vol_image;
MRSCont.coreg.vol_mask{kk} = vol_mask;
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4 changes: 4 additions & 0 deletions exampledata/ima/jobIMA.m
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Expand Up @@ -192,6 +192,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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6 changes: 5 additions & 1 deletion exampledata/nifti-mrs/jobNIfTIMRS.m
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Expand Up @@ -178,7 +178,11 @@

% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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6 changes: 5 additions & 1 deletion exampledata/p/jobP.m
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Expand Up @@ -177,7 +177,11 @@

% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/rda/jobRDA.m
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Expand Up @@ -180,6 +180,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/sdat/MEGA/jobSDAT_MEGA.m
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Expand Up @@ -191,6 +191,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m
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Expand Up @@ -191,6 +191,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/sdat/UnEdited/jobSDAT.m
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Expand Up @@ -178,6 +178,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/sdat/UnEdited_with_MM_data/jobSDAT_MM.m
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Expand Up @@ -186,6 +186,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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4 changes: 4 additions & 0 deletions exampledata/twix/jobTwix.m
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Expand Up @@ -185,6 +185,10 @@
% Optional: In case the automatic basisset picker is not working you can manually
% select the path to the basis set in the osprey/fit/basis, i.e.:
% opts.fit.basisSetFile = 'osprey/fit/basis/3T/philips/mega/press/gaba68/basis_philips_megapress_gaba68.mat';

% Optional: Deface the strucutral images in the Coreg/Seg figures for HIPAA
% compliance
opts.img.deface = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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22 changes: 20 additions & 2 deletions job/OspreyJob.m
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Expand Up @@ -210,7 +210,12 @@
fprintf('Adding macromolecule and lipid basis functions to the fit (default). Please indicate otherwise in the csv-file or the GUI \n');
MRSCont.opts.fit.fitMM = 1;
end

if isfield(jobStruct,'deface')
MRSCont.opts.img.deface = jobStruct.deface;
else
fprintf('Structrual images are not defaced (default). Please indicate otherwise in the csv-file or the GUI \n');
MRSCont.opts.img.deface = 0;
end
end

%%% 3b. LOAD JSON FILE %%%
Expand Down Expand Up @@ -388,6 +393,11 @@
opts.fit.basisSetFile = jobStruct.basisSet;
end
end
if isfield(jobStruct,'deface')
opts.img.deface = jobStruct.deface;
else
opts.img.deface = 0;
end
debug = '11';
end

Expand Down Expand Up @@ -538,7 +548,9 @@
end
if isfield(opts.fit, 'coMM3')
MRSCont.opts.fit.coMM3 = opts.fit.coMM3;
MRSCont.opts.fit.FWHMcoMM3 = opts.fit.FWHMcoMM3;
if isfield(opts.fit, 'FWHMcoMM3')
MRSCont.opts.fit.FWHMcoMM3 = opts.fit.FWHMcoMM3;
end
else
MRSCont.opts.fit.coMM3 = 'freeGauss';
MRSCont.opts.fit.FWHMcoMM3 = 14;
Expand Down Expand Up @@ -640,6 +652,12 @@
MRSCont.flags.hasStatfile = 0;
end

%Change deface option for images
if isfield(opts, 'img')
if isfield(opts.img, 'deface')
MRSCont.opts.img.deface = opts.img.deface;
end
end

%%% 5. SAVE FILE/FOLDER NAMES INTO MRSCONT %%%
% Make sure that the mandatory fields (metabolite data; output folder) are
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101 changes: 97 additions & 4 deletions load/osp_LoadNII.m
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Expand Up @@ -72,24 +72,73 @@
% Read in the raw metabolite data.
metab_ll = MRSCont.opts.MultipleSpectra.metab(ll);
raw = io_loadspec_niimrs(MRSCont.files{metab_ll,kk});
raw.flags.isUnEdited = MRSCont.flags.isUnEdited;

% If the sequence flags are not parsed form the nii header
if sum([raw.flags.isUnEdited raw.flags.isMEGA raw.flags.isHERMES raw.flags.isHERCULES]) == 0
if MRSCont.flags.isUnEdited
raw.flags.isUnEdited = 1;
end
if MRSCont.flags.isMEGA
raw.flags.isMEGA = 1;
end
if MRSCont.flags.isHERMES
raw.flags.isHERMES = 1;
end
if MRSCont.flags.isHERCULES
raw.flags.isHERCULES = 1;
end
end

% Read in the MM data.
% Leave until we have example data.

% Read in the raw water reference data.
if MRSCont.flags.hasRef
ref_ll = MRSCont.opts.MultipleSpectra.ref(ll);
raw_ref = io_loadspec_niimrs(MRSCont.files_ref{ref_ll,kk});
raw_ref.flags.isUnEdited = MRSCont.flags.isUnEdited;
% If the sequence flags are not parsed form the nii header
if sum([raw_ref.flags.isUnEdited raw_ref.flags.isMEGA raw_ref.flags.isHERMES raw_ref.flags.isHERCULES]) == 0
if MRSCont.flags.isUnEdited
raw_ref.flags.isUnEdited = 1;
end
if MRSCont.flags.isMEGA
raw_ref.flags.isMEGA = 1;
end
if MRSCont.flags.isHERMES
raw_ref.flags.isHERMES = 1;
end
if MRSCont.flags.isHERCULES
raw_ref.flags.isHERCULES = 1;
end
end

end

% Read in the short-TE water data.
if MRSCont.flags.hasWater
w_ll = MRSCont.opts.MultipleSpectra.w(ll);
raw_w = io_loadspec_niimrs(MRSCont.files_w{w_ll,kk});
raw_w.flags.isUnEdited = MRSCont.flags.isUnEdited;
% If the sequence flags are not parsed form the nii header
if sum([raw_w.flags.isUnEdited raw_w.flags.isMEGA raw_w.flags.isHERMES raw_w.flags.isHERCULES]) == 0
if MRSCont.flags.isUnEdited
raw_w.flags.isUnEdited = 1;
end
if MRSCont.flags.isMEGA
raw_w.flags.isMEGA = 1;
end
if MRSCont.flags.isHERMES
raw_w.flags.isHERMES = 1;
end
if MRSCont.flags.isHERCULES
raw_w.flags.isHERCULES = 1;
end
end

end





% Set flag and save data under appropriate name
if raw.dims.coils == 0
Expand Down Expand Up @@ -127,6 +176,28 @@
% Set flag and save data under appropriate name
if raw.dims.coils == 0
MRSCont.flags.coilsCombined = 1;
% Do some houskeeping on the metabolite data if the nii-mrs conversion
% did not work correctly
if (raw.flags.isMEGA || raw.flags.isHERMES || raw.flags.isHERCULES) && (raw.dims.subSpecs == 0)
if raw.flags.isMEGA
raw.fids = reshape(raw.fids,[raw.sz(raw.dims.t) raw.sz(raw.dims.averages)/2 2]);
raw.specs = reshape(raw.specs,[raw.sz(raw.dims.t) raw.sz(raw.dims.averages)/2 2]);
raw.averages = raw.sz(raw.dims.averages)/2;
raw.sz = size(raw.fids);
raw.subspecs = 2;
raw.rawSubspecs = 2;
raw.dims.subSpecs = 3;
end
if raw.flags.isHERMES || raw.flags.isHERCULES
raw.fids = reshape(raw.fids,[raw.sz(raw.dims.t) raw.sz(raw.dims.averages)/4 4]);
raw.specs = reshape(raw.specs,[raw.sz(raw.dims.t) raw.sz(raw.dims.averages)/4 4]);
raw.averages = raw.sz(raw.dims.averages)/4;
raw.sz = size(raw.fids);
raw.subspecs = 4;
raw.rawSubspecs = 4;
raw.dims.subSpecs = 3;
end
end
MRSCont.raw{kk} = raw;
if MRSCont.flags.hasRef
MRSCont.raw_ref{kk} = raw_ref;
Expand All @@ -135,9 +206,30 @@
if MRSCont.flags.hasWater
MRSCont.raw_w{kk} = raw_w;
end

else
MRSCont.flags.coilsCombined = 0;
% Do some houskeeping on the metabolite data if the nii-mrs conversion
% did not work correctly
if (raw.flags.isMEGA || raw.flags.isHERMES || raw.flags.isHERCULES) && (raw.dims.subSpecs == 0)
if raw.flags.isMEGA
raw.fids = reshape(raw.fids,[raw.sz(raw.dims.t) raw.sz(raw.dims.coils) raw.sz(raw.dims.averages)/2 2]);
raw.specs = reshape(raw.specs,[raw.sz(raw.dims.t) raw.sz(raw.dims.coils) raw.sz(raw.dims.averages)/2 2]);
raw.averages = raw.sz(raw.dims.averages)/2;
raw.sz = size(raw.fids);
raw.subspecs = 2;
raw.rawSubspecs = 2;
raw.dims.subSpecs = 4;
end
if raw.flags.isHERMES || raw.flags.isHERCULES
raw.fids = reshape(raw.fids,[raw.sz(raw.dims.t) raw.sz(raw.dims.coils) raw.sz(raw.dims.averages)/4 4]);
raw.specs = reshape(raw.specs,[raw.sz(raw.dims.t) raw.sz(raw.dims.coils) raw.sz(raw.dims.averages)/4 4]);
raw.averages = raw.sz(raw.dims.averages)/4;
raw.sz = size(raw.fids);
raw.subspecs = 4;
raw.rawSubspecs = 4;
raw.dims.subSpecs = 4;
end
end
MRSCont.raw_uncomb{kk} = raw;
if MRSCont.flags.hasRef
MRSCont.raw_ref_uncomb{kk} = raw_ref;
Expand All @@ -147,6 +239,7 @@
MRSCont.raw_w_uncomb{kk} = raw_w;
end
end

end
% Try to get some params from NIFTI
if isfield(raw.nii_mrs.hdr_ext,'Manufacturer')
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1 change: 1 addition & 0 deletions settings/OspreySettings.m
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Expand Up @@ -49,6 +49,7 @@
MRSCont.opts.ECC.mm = 1; % Do ECC for all metabolite-nulled spectra.
MRSCont.opts.cosmetics.LB = 0; % Do cosmetic LB
MRSCont.opts.cosmetics.Zoom = 2.75; % Do cosmetic Zoom
MRSCont.opts.img.deface = 0; % Deface data
%%% 2. FIND AND SET PATHS %%%
% Osprey
[settingsFolder,~,~] = fileparts(which('OspreySettings.m'));
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2 changes: 1 addition & 1 deletion utilities/RunOspreyJob.m
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Expand Up @@ -7,7 +7,7 @@
% MRSCont = RunOspreyJob(jobFilePath)
%
% INPUTS:
% jobFilePath = path to the Osprey jobfile (.m, .csv or .jason).
% jobFilePath = path to the Osprey jobfile (.m, .csv or .json).
%
% OUTPUTS:
% MRSCont = Osprey MRS data container.
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