How to convert .mat to .nii?

Hi!

I have a set of .mat files and I would like to convet them to .nii (Nifti) to conduct some GLM analysis.

The problem I have with these files is that when I load them in MATLAB, they are 1x111 cell. When I open a cell, it is 1x1435 double.

I tried converting them using make_nii but it tells me the files are not in the correct format. Any suggestions about how to do this?

Thank you so much,

Carlotta.

Answer 1

[Anudeep Kumar]

Hi Carlotta,

I believe the issue lies in the input not being of the shape as expected by ‘make_nii’ function. The .nii files are expected to be 2D/3D/4D arrays. You can achieve this by reshaping your cell into a 2D or 3D or 4D data based on your use case

According to the information provided we can reshape your data into a 2D array of size 111x1435 using ‘cell2mat’ and save it as nii.

Below is a short code snippet to do the same:

% Load the .mat file
data = load('example_data.mat');
mycell = data.example_cells; % Use the variable name from the .mat file

% Convert to matrix [111 x 1435]
mat_data = cell2mat(mycell'); % Transpose to get [111 x 1435]

nii = make_nii(mat_data);
save_nii(nii, 'example_output.nii');

You can reshape your data using ‘reshape’ to convert data into 3D as below :

% For demonstration, let's reshape to [35, 41, 111] since 35*41=1435
mat_data_reshaped = reshape(mat_data, [111, 35,41]);
mat_data_reshaped = permute(mat_data_reshaped, [2, 3, 1]); % [X Y T]

Here are the documentations for ‘cell2mat’, ’reshape’, and ‘permute‘ for your better understanding of these functions and use them as per your requirement.

https://www.mathworks.com/help/releases/R2024b/matlab/ref/cell2mat.html

https://www.mathworks.com/help/releases/R2024b/matlab/ref/double.reshape.html

https://www.mathworks.com/help/releases/R2024b/matlab/ref/double.permute.html

Hope this helps!