Bugfix: Running CAT12 and SimNIBS with files without sform/qform

toolbox/anatomy/mri_add_world.m

@@ -0,0 +1,43 @@
+function sMri = mri_add_world(MriFile, sMri)
+% MRI_ADD_WORLD: Add a default "world" transformation to a MRI.
+
+% @=============================================================================
+% This function is part of the Brainstorm software:
+% https://neuroimage.usc.edu/brainstorm
+% 
+% Copyright (c) University of Southern California & McGill University
+% This software is distributed under the terms of the GNU General Public License
+% as published by the Free Software Foundation. Further details on the GPLv3
+% license can be found at http://www.gnu.org/copyleft/gpl.html.
+% 
+% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
+% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
+% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
+% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
+% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
+%
+% For more information type "brainstorm license" at command prompt.
+% =============================================================================@
+%
+% Authors: Francois Tadel, 2023
+
+% If MRI is not loaded yet
+if (nargin < 2) || isempty(sMri)
+    sMri = in_mri_bst(MriFile);
+end
+
+% A vox2ras matrix must be present in the MRI for running CAT12
+if ~isfield(sMri, 'InitTransf') || isempty(sMri.InitTransf) || ~any(strcmpi(sMri.InitTransf(:,1), 'vox2ras'))
+    disp('BST> Adding default world transformation to MRI...');
+    % Add vox2ras
+    sMri.InitTransf = {'vox2ras', ...
+        [1, 0, 0, -size(sMri.Cube,1) / 2 .* sMri.Voxsize(1); ...
+         0, 1, 0, -size(sMri.Cube,2) / 2 .* sMri.Voxsize(2); ...
+         0, 0, 1, -size(sMri.Cube,3) / 2 .* sMri.Voxsize(3); ...
+         0, 0, 0, 1]};
+    % Remove existing NIFTI header because it would cause incompatibilities
+    sMri.Header = [];
+    % Save modification
+    bst_save(file_fullpath(MriFile), sMri, 'v7');
+end
+

toolbox/io/import_anatomy_cat_2020.m

@@ -262,6 +262,8 @@
         return;
     end
 end
+% Load file again, to get the new fiducials
+sMri = in_mri_bst(BstT1File);
 
 
 %% ===== MNI NORMALIZATION =====

toolbox/process/functions/process_fem_mesh.m

@@ -260,6 +260,8 @@
             errMsg = 'Invalid neck MNI Z coordinate (must be negative or zero).';
             return;
         end
+        % A vox2ras matrix must be present in the MRI
+        sMriT1 = mri_add_world(T1File, sMriT1);
     end
 
     % ===== LOAD/CUT T2 =====
@@ -279,6 +281,8 @@
                 sMriT2 = sMriT2tmp;
             end
         end
+        % A vox2ras matrix must be present in the MRI
+        sMriT2 = mri_add_world(T2File, sMriT2);
     end
     FemFile = [];
 
@@ -750,12 +754,17 @@
             % Create temporary folder for segmentation files
             simnibsDir = bst_fullfile(bst_get('BrainstormTmpDir'), simCmd);
             mkdir(simnibsDir);
+            % Remove previous nifti header, as it can cause issues with SimNIBS (if sform is defined and not qform)
+            sMriT1.Header = [];
             % Save T1 MRI in .nii format
             subjid = strrep(sSubject.Name, '@', '');
             T1Nii = bst_fullfile(simnibsDir, [subjid 'T1.nii']);
             out_mri_nii(sMriT1, T1Nii);
             % Save T2 MRI in .nii format
             if ~isempty(T2File)
+                % Remove previous nifti header, as it can cause issues with SimNIBS (if sform is defined and not qform)
+                sMriT2.Header = [];
+                % Save file
                 T2Nii = bst_fullfile(simnibsDir, [subjid 'T2.nii']);
                 out_mri_nii(sMriT2, T2Nii);
             else

toolbox/process/functions/process_segment_cat12.m

@@ -23,7 +23,7 @@
 % For more information type "brainstorm license" at command prompt.
 % =============================================================================@
 %
-% Authors: Francois Tadel, 2019-2021
+% Authors: Francois Tadel, 2019-2023
 
 eval(macro_method);
 end
@@ -242,6 +242,8 @@
                 'Missing fiducials: the surfaces cannot be aligned with the MRI.'];
         end
     end
+    % A vox2ras matrix must be present in the MRI for running CAT12
+    sMri = mri_add_world(T1FileBst, sMri);
 
     % ===== SAVE MRI AS NII =====
     bst_progress('text', 'Saving temporary files...');