Add ct2mrireg plugin (#654)

* Add "ct2mrireg" as a plugin to perform CT to MRI co-registration --------- Co-authored-by: rcassani <[email protected]>
brainstorm-tools · Nov 9, 2023 · c5ffb02 · c5ffb02
1 parent 259c409
commit c5ffb02
Show file tree

Hide file tree

Showing 4 changed files with 99 additions and 9 deletions.
diff --git a/toolbox/anatomy/mri_coregister.m b/toolbox/anatomy/mri_coregister.m
@@ -38,6 +38,7 @@
 % =============================================================================@
 %
 % Authors: Francois Tadel, 2016-2023
+%          Chinmay Chinara, 2023
 
 % ===== LOAD INPUTS =====
 % Parse inputs
@@ -233,7 +234,60 @@
         end
         % Output file tag
         fileTag = '_mni';
+
+    % ===== CT2MRIREG =====
+    case 'ct2mri'
+        % Check if ct2mrireg plugin is installed
+        [isInstalled, errMsg] = bst_plugin('Install', 'ct2mrireg');
+        if ~isInstalled
+            if ~isProgress
+                bst_progress('stop');
+            end
+            return;
+        end
+
+        % Save files in tmp directory
+        bst_progress('text', 'Saving temporary files...');
+        % Get temporary folder
+        TmpDir = bst_get('BrainstormTmpDir', 0, 'ct2mrireg');
+        % Save source CT in .nii format
+        NiiSrcFile = bst_fullfile(TmpDir, 'ct2mri_src.nii');
+        out_mri_nii(sMriSrc, NiiSrcFile);
+        % Save reference MRI in .nii format
+        NiiRefFile = bst_fullfile(TmpDir, 'ct2mri_ref.nii');
+        out_mri_nii(sMriRef, NiiRefFile);
+
+        % Save registered file in .nii.gz format
+        NiiRegFile = bst_fullfile(TmpDir, 'contrastmri2preMRI.nii.gz');
+        bst_progress('text', 'Performing co-registration using ct2mrireg plugin...');
+        NiiRegFile = ct2mrireg(NiiSrcFile, NiiRefFile, NiiRegFile);
+
+        % Read output volume
+        sMriReg = in_mri(NiiRegFile, 'ALL', 0, 0);
+
+        % Delete the temporary files
+        file_delete(TmpDir, 1, 1);
+        % Output file tag
+        fileTag = '_ct2mri';
 
+        % === UPDATE FIDUCIALS ===
+        if isReslice
+            % Use the reference SCS coordinates
+            if isfield(sMriRef, 'SCS')
+                sMriReg.SCS = sMriRef.SCS;
+            end
+            % Use the reference NCS coordinates
+            if isfield(sMriRef, 'NCS')
+                sMriReg.NCS = sMriRef.NCS;
+            end
+
+            % Reslice the volume
+            [sMriReg, errMsg] = mri_reslice(sMriReg, sMriRef, 'scs', 'scs', isAtlas);
+        else
+            isUpdateScs = 1;
+            isUpdateNcs = 1;
+        end
+
     % ===== VOX2RAS =====
     case 'vox2ras'
         % Nothing to do, just reslice if needed

diff --git a/toolbox/core/bst_plugin.m b/toolbox/core/bst_plugin.m
@@ -105,7 +105,7 @@
 % For more information type "brainstorm license" at command prompt.
 % =============================================================================@
 %
-% Authors: Francois Tadel 2021-2023
+% Authors: Francois Tadel, 2021-2023
 
 eval(macro_method);
 end
@@ -192,6 +192,20 @@
     PlugDesc(end).UnloadPlugs    = {'spm12', 'iso2mesh'};
     PlugDesc(end).LoadFolders    = {'lib/spm12', 'lib/iso2mesh', 'lib/cvx', 'lib/ncs2daprox', 'lib/NIFTI_20110921'};
 
+    % === ANATOMY: CT2MRIREG ===
+    % this plugin is used for performing CT to MRI co-registration
+    PlugDesc(end+1)              = GetStruct('ct2mrireg');
+    PlugDesc(end).Version        = 'github-master';
+    PlugDesc(end).Category       = 'Anatomy';
+    PlugDesc(end).AutoUpdate     = 1;
+    PlugDesc(end).URLzip         = 'https://github.com/ajoshiusc/USCCleveland/archive/master.zip';
+    PlugDesc(end).URLinfo        = 'https://github.com/ajoshiusc/USCCleveland/tree/master/ct2mrireg';
+    PlugDesc(end).TestFile       = 'ct2mrireg.m';
+    PlugDesc(end).ReadmeFile     = 'ct2mrireg/README.md';
+    PlugDesc(end).CompiledStatus = 2;
+    PlugDesc(end).LoadFolders    = {'ct2mrireg'};
+    PlugDesc(end).DeleteFiles    = {'fmri_analysis', 'for_clio', 'mixed_atlas', 'process_script', 'reg_prepost', 'visualize_channels', '.gitignore', 'README.md'};
+
     % === FORWARD: OPENMEEG ===
     PlugDesc(end+1)              = GetStruct('openmeeg');
     PlugDesc(end).Version        = '2.4.1';

diff --git a/toolbox/io/import_mri.m b/toolbox/io/import_mri.m
@@ -1,5 +1,5 @@
 function [BstMriFile, sMri, Messages] = import_mri(iSubject, MriFile, FileFormat, isInteractive, isAutoAdjust, Comment, Labels)
-% IMPORT_MRI: Import a MRI file in a subject of the Brainstorm database
+% IMPORT_MRI: Import a volume file (MRI, Atlas, CT, etc) in a subject of the Brainstorm database
 % 
 % USAGE: [BstMriFile, sMri, Messages] = import_mri(iSubject, MriFile, FileFormat='ALL', isInteractive=0, isAutoAdjust=1, Comment=[], Labels=[])
 %               BstMriFiles = import_mri(iSubject, MriFiles, ...)   % Import multiple volumes at once
@@ -38,6 +38,7 @@
 % =============================================================================@
 %
 % Authors: Francois Tadel, 2008-2023
+%          Chinmay Chinara, 2023
 
 %% ===== PARSE INPUTS =====
 if (nargin < 3) || isempty(FileFormat)
@@ -69,6 +70,15 @@
 else
     sSubject = ProtocolSubjects.Subject(iSubject);
 end
+% Volume type
+volType = 'MRI';
+if ~isempty(strfind(Comment, 'CT'))
+    volType = 'CT';
+end
+% Get node comment from filename
+if ~isempty(strfind(Comment, 'Import'))
+    Comment = [];
+end
 
 %% ===== SELECT MRI FILE =====
 % If MRI file to load was not defined : open a dialog box to select it
@@ -80,9 +90,10 @@
     if isempty(DefaultFormats.MriIn)
         DefaultFormats.MriIn = 'ALL';
     end
-    % Get MRI file
+
+    % Get MRI/CT file
     [MriFile, FileFormat, FileFilter] = java_getfile( 'open', ...
-        'Import MRI...', ...              % Window title
+        ['Import ' volType '...'], ...   % Window title
         LastUsedDirs.ImportAnat, ...      % Default directory
         'multiple', 'files_and_dirs', ... % Selection mode
         bst_get('FileFilters', 'mri'), ...
@@ -140,7 +151,7 @@
 %% ===== LOAD MRI FILE =====
 isProgress = bst_progress('isVisible');
 if ~isProgress
-    bst_progress('start', 'Import MRI', 'Loading MRI file...');
+    bst_progress('start', ['Import ', volType], ['Loading ', volType, ' file...']);
 end
 % MNI / Atlas?
 isMni = ismember(FileFormat, {'ALL-MNI', 'ALL-MNI-ATLAS'});
@@ -215,7 +226,8 @@
     else
         % If some transformation where made to the intial volume: apply them to the new one ?
         if isfield(sMriRef, 'InitTransf') && ~isempty(sMriRef.InitTransf) && any(ismember(sMriRef.InitTransf(:,1), {'permute', 'flipdim'}))
-            if ~isInteractive || java_dialog('confirm', ['A transformation was applied to the reference MRI.' 10 10 'Do you want to apply the same transformation to this new volume?' 10 10], 'Import MRI')
+            isApplyTransformation = java_dialog('confirm', ['A transformation was applied to the reference MRI.' 10 10 'Do you want to apply the same transformation to this new volume?' 10 10], ['Import ', volType]);
+            if ~isInteractive || isApplyTransformation
                 % Apply step by step all the transformations that have been applied to the original MRI
                 for it = 1:size(sMriRef.InitTransf,1)
                     ttype = sMriRef.InitTransf{it,1};
@@ -253,11 +265,17 @@
             % Register with the MNI transformation
             strOptions = [strOptions, '<BR>- <U><B>MNI</B></U>:&nbsp;&nbsp;&nbsp;Compute the MNI transformation for both volumes (inaccurate).'];
             cellOptions{end+1} = 'MNI';
+            if strcmpi(volType, 'CT')
+                % Register with the ct2mrireg plugin
+                strOptions = [strOptions, '<BR>- <U><B>CT2MRI</B></U>:&nbsp;&nbsp;&nbsp;Coregister using USC ct2mrireg plugin.'];
+                cellOptions{end+1} = 'CT2MRI';
+            end
             % Skip registration
             strOptions = [strOptions, '<BR>- <U><B>Ignore</B></U>:&nbsp;&nbsp;&nbsp;The two volumes are already registered.'];
             cellOptions{end+1} = 'Ignore';
             % Ask user to make a choice
-            RegMethod = java_dialog('question', [strOptions '<BR><BR></HTML>'], 'Import MRI', [], cellOptions, 'Reg+reslice');
+            RegMethod = java_dialog('question', [strOptions '<BR><BR></HTML>'], ['Import ', volType], [], cellOptions, 'Reg+reslice');
+
         % In non-interactive mode: ignore if possible, or use the first option available
         else
             RegMethod = 'Ignore';
@@ -283,9 +301,9 @@
             % Ask to reslice
             isReslice = java_dialog('confirm', [...
                 '<HTML><B>Reslice the volume?</B><BR><BR>' ...
-                'This operation rewrites the new MRI to match the alignment, <BR>size and resolution of the original volume.' ...
+                ['This operation rewrites the new ', volType, ' to match the alignment, <BR>size and resolution of the original volume.'] ...
                 strSizeWarn ...
-                '<BR><BR></HTML>'], 'Import MRI');
+                '<BR><BR></HTML>'], ['Import ', volType]);
         % In non-interactive mode: never reslice
         else
             isReslice = 0;
@@ -299,6 +317,9 @@
             case 'SPM'
                 % Register the new MRI on the existing one using SPM + RESLICE
                 [sMri, errMsg, fileTag] = mri_coregister(sMri, sMriRef, 'spm', isReslice, isAtlas);
+            case 'CT2MRI'
+                % Register the CT to excisting MRI using USC's ct2mrireg plugin
+                [sMri, errMsg, fileTag] = mri_coregister(sMri, sMriRef, 'ct2mri', isReslice, isAtlas);
             case 'Ignore'
                 if isReslice
                     % Register the new MRI on the existing one using the transformation in the input files (files already registered)

diff --git a/toolbox/tree/tree_callbacks.m b/toolbox/tree/tree_callbacks.m
@@ -562,6 +562,7 @@
                     gui_component('MenuItem', jPopup, [], 'Import anatomy folder', IconLoader.ICON_ANATOMY, [], @(h,ev)bst_call(@import_anatomy, iSubject, 0));
                     gui_component('MenuItem', jPopup, [], 'Import anatomy folder (auto)', IconLoader.ICON_ANATOMY, [], @(h,ev)bst_call(@import_anatomy, iSubject, 1));
                     gui_component('MenuItem', jPopup, [], 'Import MRI', IconLoader.ICON_ANATOMY, [], @(h,ev)bst_call(@import_mri, iSubject, [], [], 1));
+                    gui_component('MenuItem', jPopup, [], 'Import CT', IconLoader.ICON_ANATOMY, [], @(h,ev)bst_call(@import_mri, iSubject, [], [], 1, 1, 'Import CT'));
                     gui_component('MenuItem', jPopup, [], 'Import surfaces', IconLoader.ICON_SURFACE, [], @(h,ev)bst_call(@import_surfaces, iSubject));
                     gui_component('MenuItem', jPopup, [], 'Import fibers', IconLoader.ICON_FIBERS, [], @(h,ev)bst_call(@import_fibers, iSubject));
                     gui_component('MenuItem', jPopup, [], 'Convert DWI to DTI', IconLoader.ICON_FIBERS, [], @(h,ev)bst_call(@process_dwi2dti, 'ComputeInteractive', iSubject));