Add PET volume processing: SUVR, ROI masking, projection to surface, SPM-petpve plugin #798
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…_plugin
- Added PETPVE12 as a supported plugin in GetSupported(), with download URL, test file, and documentation.
- Extended LinkSpmToolbox (formerly LinkCatSpm) to handle both CAT12 and PETPVE12 using action codes:
- 0/1/2 for CAT12 (delete/create/check link)
- 3/4/5 for PETPVE12 (delete/create/check link)
- Updated InstalledFcn, UninstalledFcn, and LoadedFcn for both CAT12 and PETPVE12 to use the new LinkSpmToolbox action codes.
- Ensured plugin installation, linking, and uninstallation workflows are consistent for both toolboxes.
- Maintained backward compatibility for CAT12 and verified no regression/breaking in its functionality.
…alues in volume files. Primarily intended for calculating standardized uptake value ratios in PET volumes. - Rescales volumes by the mean value of a specified ROI from an atlas. - Supports both file and structure input, with optional subject context for structure input. - Uses atlas region labels (from bst_get) for robust and consistent ROI selection. - Handles output as either a new file (with unique file tag inserted before the last underscore-tag) or as a structure. - Returns atlas labels, output file/struct, error message, and file tag for downstream processing. - Designed to integrate with mri_mask and Brainstorm's subject/anatomy management. - Enables flexible atlas-based PET/MRI SUVR normalization.
…pting/pipelines - Iprocess_pet, a pipeline function for PET volume processing, for sequencing atlas-based SUVR rescaling and/or masking in a single workflow. - process_pet minimizes redundant file saving by chaining operations in memory and saving the final result, with proper file tagging and history. - Displays the processed PET volume on the subject's default MRI for immediate visualization. - panel_process_pet GUI to collect user options and call process_pet, enabling user-friendly PET processing from the Brainstorm interface.
- mri_interp_vol2tess projects MRI/PET/CT volumes onto cortical surfaces (pial, mid, white) using weighted interpolation, - Enhanced panel_process_pet GUI: added "Project to surface" option - Updated process_pet pipeline to accept and pass projection command to mri_interp_vol2tess.
- Added logic in bst_get to retrieve subject's atlas structures, including support for atlas label queries and subject context. Added a new function, mri_mask, which enables masking of MRI volumes based on existing atlas regions. mri_mask uses atlas label lists from bst_get to obtain ROIs. - mri_mask supports both file and structure input, outputs the masked MRI (file or struct), the file tag, and the binary mask used. - mri_mask can be used to list available atlas regions in a given atlas file for the subject, generate a binary mask for a selected region, or save a masked MRI volume to disk, with full subject and atlas context. - These changes add ROI-based masking functions and flexibility for atlas-based workflows in Brainstorm volumes
…mri_interp_vol2tess.
…UI for masking, SUVR calculation and surface projection
- Same action number regardless the Toolbox - Toolbox name as argument - Delete link when Unloading Toolbox (in case SPM is still loaded) - Test installation wint `TestFile`
- Remove duplicated callback - Remove unused arg in AtlasChanged_Callback - Align for easier reading
e.g: From: `18Fflortaucipir_pet_spm_reslice_rescaled_aseg_cerebellum_masked_aseg_cerebellum_rescaled_aseg_cerebellum_masked_aseg_brainmask` To: `18Fflortaucipir_pet_spm_reslice_masked_aseg_cerebellum_rescaled_aseg_cerebellum_masked_aseg_brainmask`
rcassani
reviewed
Jun 3, 2025
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Hi @DiellorBasha, everything looks fine
Just some questions to address before merging
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| % - MriFileSrc : Source MRI file | ||
| % - MriFileRef : Reference MRI file | ||
| % - Condition : Condition name for the projection | ||
| % - TimeVector : Time vector for the results | ||
| % - DisplayUnits: |
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Description for DisplayUnits and ProjFrac are missing
| vol2tess_mat = cell2mat(vol2tess); | ||
| map = vol2tess_mat * ProjFrac'; | ||
| else | ||
| error('Surface vertex counts do not match. Cannot combine projections.'); |
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If we only consider the option of one "time" sample.
Why do we even have Time vector as input?
toolbox/tree/tree_callbacks.m
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| gui_component('MenuItem', jMenu, [], 'Realign frames', IconLoader.ICON_VOLPET, [], @(h,ev)PetImportProcess_Callback(PetFile)); | ||
| % === PET PROCESSING === | ||
| AddSeparator(jMenu); | ||
| gui_component('MenuItem', jMenu, [], 'Process volume', IconLoader.ICON_VOLPET, [], @(h,ev)bst_call(@gui_show_dialog, 'PET processing options', @panel_process_pet, 1, [], sSubject, PetFile)); |
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Would a more specific name such as Compute SUVR values be ok?
Process volume is quite vague
| % === PET PROCESSING === | ||
| AddSeparator(jMenu); | ||
| gui_component('MenuItem', jMenu, [], 'Process volume', IconLoader.ICON_VOLPET, [], @(h,ev)bst_call(@gui_show_dialog, 'PET processing options', @panel_process_pet, 1, [], sSubject, PetFile)); | ||
| gui_component('MenuItem', jMenu, [], 'Project to surface', IconLoader.ICON_SURFACE_CORTEX, [], @(h,ev)bst_call(@mri_interp_vol2tess, PetFile, [], 'PET')); |
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Maybe Project volume to surface as option name?
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| % === ANATOMY: PETPVE12 === | ||
| PlugDesc(end+1) = GetStruct('petpve12'); | ||
| PlugDesc(end).Version = 'latest'; | ||
| PlugDesc(end).Category = 'Anatomy'; | ||
| PlugDesc(end).AutoUpdate = 1; | ||
| PlugDesc(end).URLzip = 'https://github.com/GGonEsc/petpve12/archive/refs/heads/master.zip'; | ||
| PlugDesc(end).URLinfo = 'https://multimodalneuroimaging.wordpress.com/software/'; | ||
| PlugDesc(end).TestFile = 'tbx_cfg_petpve12.m'; | ||
| PlugDesc(end).ReadmeFile = 'Contents.m'; | ||
| PlugDesc(end).CompiledStatus = 0; | ||
| PlugDesc(end).RequiredPlugs = {'spm12'}; | ||
| PlugDesc(end).InstalledFcn = 'LinkSpmToolbox(1, ''petpve12'');'; | ||
| PlugDesc(end).UninstalledFcn = 'LinkSpmToolbox(0, ''petpve12'');'; | ||
| PlugDesc(end).LoadedFcn = 'LinkSpmToolbox(2, ''petpve12'');'; | ||
| PlugDesc(end).UnloadedFcn = 'LinkSpmToolbox(0, ''petpve12'');'; | ||
| PlugDesc(end).ExtraMenus = {'Online tutorial', 'web(''https://github.com/GGonEsc/petpve12/blob/master/help/PETPVE12_manual.pdf'', ''-browser'')'}; | ||
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SPM toolbox PETPVE12 is added as Brainstorm plugin.
However, this is never used, does this belongs to a future development?
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Ping @DiellorBasha |
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PET processing functionalities, extending the previously integrated PET import pipeline.
Features:
New functions:
process_pet.m: scriptable entry point for PET processing - used to chain together PET processing functionspanel_process_pet.m: GUI for collecting user input for PET processing - works withprocess_pet.mmri_rescale.m: rescale intensity values (e.g. SUV/SUVR) using the mean value of a reference regions - works withpanel_process_pet.mandmri_mask.mmri_mask.m: bilateral ROI-based volume masking using atlas labels from supported atlases: "aseg", "Desikan-Killiany" and so on.mri_interp_vol2tess.m: interpolates 3D PET volumes onto cortical surfacesPlease let me know if further modularization or code cleanup is needed. Thanks for reviewing!