Save maps

[NicoloPecco]

Hi Marco,

I was wondering if it is possible to save all of the maps (CBV, CBF etc.) without loosing the nifti header information of the input file (dsc.nii). This step allows to visualize the maps in the same space of the input.

Thank you in advance,

Nicolo

[marcocastellaro]

Dear Nicolo,

I have added here [https://github.com/marcocastellaro/dsc-mri-toolbox/commit/9e1e8cc7349d00ed269072d1fc85cbdb9f754339]

some code in the demo that does the save of the cbv map. just change the map you want to save and enjoy.

Let me know if everything is ok.

[nyoman1994]

Hi Marco, Sorry I could not get saving the map for the CBF and MTT to work.. Are there other steps I miss?

Thank you, Nyoman

nifti_template = DSC_info; nifti_template.Datatype='double'; nifti_template.BitsPerPixel=64; nifti_template.ImageSize=size(cbf); niftiwrite(cbf,fullfile('demo-data','cbf.nii'),nifti_template) Error using niftiwrite>parseInputs (line 151) The input volume must be specified as a numeric matrix.

Error in niftiwrite (line 89) [V, path, filename, params] = parseInputs(V, filename, varargin{:});

[Marijn311]

This is the code I used to save all output maps

% ------ Save all 3D spatial results in NIFTI format --------------------- nifti_template = DSC_info; nifti_template.Datatype='double'; nifti_template.BitsPerPixel=64; nifti_template.ImageSize=size(cbv); nifti_template.PixelDimensions=nifti_template.PixelDimensions(1:3); % remove time dimension

niftiwrite(cbv,fullfile(DSC_folder_path, 'CBV.nii'),nifti_template) niftiwrite(cbv_lc,fullfile(DSC_folder_path, 'CBV_lc.nii'),nifti_template) niftiwrite(ttp,fullfile(DSC_folder_path, 'TTP.nii'),nifti_template) niftiwrite(mask,fullfile(DSC_folder_path, 'mask.nii'),nifti_template) niftiwrite(s0,fullfile(DSC_folder_path, 'S0.nii'),nifti_template) niftiwrite(cbf.svd.map,fullfile(DSC_folder_path, 'CBF.nii'),nifti_template) niftiwrite(mtt.svd,fullfile(DSC_folder_path, 'MTT.nii'),nifti_template)

[nyoman1994]

Hi Marijn, Thanks very much for this.

Actually I have another question regarding the results… Is there a documentation for the results Units (CBV, CBF, MTT)?

Regards, Nyoman

On 12 Nov 2024, at 23:28, Marijn Borghouts @.***> wrote:

This is the code I used to save all output maps

% ------ Save all 3D spatial results in NIFTI format --------------------- nifti_template = DSC_info; nifti_template.Datatype='double'; nifti_template.BitsPerPixel=64; nifti_template.ImageSize=size(cbv); nifti_template.PixelDimensions=nifti_template.PixelDimensions(1:3); % remove time dimension

niftiwrite(cbv,fullfile(DSC_folder_path, 'CBV.nii'),nifti_template) niftiwrite(cbv_lc,fullfile(DSC_folder_path, 'CBV_lc.nii'),nifti_template) niftiwrite(ttp,fullfile(DSC_folder_path, 'TTP.nii'),nifti_template) niftiwrite(mask,fullfile(DSC_folder_path, 'mask.nii'),nifti_template) niftiwrite(s0,fullfile(DSC_folder_path, 'S0.nii'),nifti_template) niftiwrite(cbf.svd.map,fullfile(DSC_folder_path, 'CBF.nii'),nifti_template) niftiwrite(mtt.svd,fullfile(DSC_folder_path, 'MTT.nii'),nifti_template)

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