Merge pull request #552 from HJZollner/develop

[Feature Request] - Defacing of structural images - OspreyCoreg/Seg -…
schorschinho · Feb 1, 2023 · 8499e3f · 8499e3f
2 parents d2b2ec8 + fc89806
commit 8499e3f
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Showing 15 changed files with 168 additions and 9 deletions.
diff --git a/coreg/OspreyCoreg.m b/coreg/OspreyCoreg.m
@@ -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;

diff --git a/exampledata/ima/jobIMA.m b/exampledata/ima/jobIMA.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/nifti-mrs/jobNIfTIMRS.m b/exampledata/nifti-mrs/jobNIfTIMRS.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/p/jobP.m b/exampledata/p/jobP.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/rda/jobRDA.m b/exampledata/rda/jobRDA.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/sdat/MEGA/jobSDAT_MEGA.m b/exampledata/sdat/MEGA/jobSDAT_MEGA.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m b/exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/sdat/UnEdited/jobSDAT.m b/exampledata/sdat/UnEdited/jobSDAT.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/sdat/UnEdited_with_MM_data/jobSDAT_MM.m b/exampledata/sdat/UnEdited_with_MM_data/jobSDAT_MM.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/exampledata/twix/jobTwix.m b/exampledata/twix/jobTwix.m
@@ -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;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 

diff --git a/graphics/osprey.jpeg b/graphics/osprey.jpeg
diff --git a/job/OspreyJob.m b/job/OspreyJob.m
@@ -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 %%%
@@ -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
 
@@ -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;
@@ -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

diff --git a/load/osp_LoadNII.m b/load/osp_LoadNII.m
@@ -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
@@ -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;
@@ -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;
@@ -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')

diff --git a/settings/OspreySettings.m b/settings/OspreySettings.m
@@ -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'));

diff --git a/utilities/RunOspreyJob.m b/utilities/RunOspreyJob.m
@@ -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.