Trouble writing and saving .nii files

Hi @Grace,

In order to resolve this issue, I will suggest a revised approach:

When extracting each flip angle’s data for saving, directly access it without reshaping unnecessarily and modify your saving loop, here is modified code snippet,

       for i = 1:size(T1, 4)

       % Directly convert the T1 data for this angle

       Data = double(T1(:, :, :, i));

       % Define voxel size

       VoxSize = [0.6, 0.6, 1];

       % Create a name for the NIfTI file

       NameForSaving = sprintf('T1_Map_Angle%d.nii', i);

       % Define the file location for saving

       filelocation = 'location_hidden';

       fullpath = fullfile(filelocation, NameForSaving);

       % Save the data as a NIfTI file using Nii_Saver

       Nii_Saver(Data, VoxSize, fullpath);

       end

Make sure that `Nii_Saver` correctly interprets the dimensions of `Data`. If it expects a specific orientation or arrangement of dimensions (e.g., [X,Y,Z]), make sure that you are providing it in that format.After saving each file, it might be beneficial to load them back into MATLAB using a tool like `niftiread` to verify their integrity and correct dimensionality before moving on to visualization in FSLeyes. Hope this helps.

Hi @Grace,

Here’s an adjusted code snippet that keeps the original structure while saving:

    for i = 1:size(T1, 4)

    % Directly convert the T1 data for this angle

    Data = double(T1(:, :, :, i)); % This extracts the correct angle

    % Define voxel size

    VoxSize = [0.6, 0.6, 1];

    % Create a name for the NIfTI file

    NameForSaving = sprintf('T1_Map_Angle%d.nii', i);

    % Define the file location for saving

    filelocation = 'location_hidden';

    fullpath = fullfile(filelocation, NameForSaving);

    % Save the data as a NIfTI file using Nii_Saver

    Nii_Saver(Data, VoxSize, fullpath);

     end

If reordering is necessary (to get slices organized as 1,2,...170 for each angle), consider implementing a more explicit reordering function before saving:

    for i = 1:size(T1, 4)

    Data = double(T1(:, :, :, i));

    % Assuming you want to rearrange slices

    reorderedData = reshape(permute(Data, [1, 2, 4, 3]), [512, 512,     170]);

    VoxSize = [0.6, 0.6, 1];

    NameForSaving = sprintf('T1_Map_Angle%d.nii', i);

    fullpath = fullfile(filelocation, NameForSaving);

    Nii_Saver(reorderedData, VoxSize, fullpath);

    end

Before running on your complete dataset, consider testing with smaller sample arrays to confirm that your process works as expected without introducing errors into your T1 values. I will wait for @Cris LaPierre suggestion.

Hi @Grace,

Based on your description, if I comprehend correctly, it seems like you are trying to rearrange your data in a specific order after performing calculations. You want to display the slices in the order of 1, 2, 3, 4, 5...170 instead of the current order of 1, 6, 11, 16...2, 7, 12, 17...3, 8, 13, 18...4, 9, 14, 19...5, 10, 15, 20...170. To achieve this task, you can use indexing and reshaping operations. Here's an example code that demonstrates how you can rearrange the data:

   % Assuming your data is stored in a variable called 'T1'

   % Get the size of your data

    [height, width, slices_per_angle, num_angles] = size(T1);

   % Reshape the data to [height x width x (slices_per_angle * 

   num_angles)]

   reshaped_data = reshape(T1, [height, width, slices_per_angle * 

   num_angles]);

   % Rearrange the slices to the desired order

   new_order = reshape(1:slices_per_angle*num_angles, 

   [num_angles,slices_per_angle]);

   new_order = new_order'; % Transpose to match desired order

   % Index and select slices according to the new order

   rearranged_data = reshaped_data(:, :, new_order(:), :);

So, as you can see, I reshaped the original data `T1` into a new shape where all the slices are concatenated together, then created a matrix `new_order` that represents the desired order of the slices. By indexing with `new_order(:)`, you can select and rearrange the slices accordingly.This should result in `rearranged_data` having the desired order of slices: 1, 2, 3, 4, 5...170. I assume your data is stored in a four-dimensional array with dimensions `[height x width x slices_per_angle x num_angles]` because adjustments may be needed if your data is organized differently.

I will assume @Cris LaPierre probably have a different approach. For now, this should help. Please let me know if you have any further questions.

Hi @ Cris LaPierre,

To save each angle from a 4D array as individual NIfTI files, here is the code snippet.

% Assuming 'data' is your 4D array with dimensions [height, width, 

slices_per_angle, num_angles]

[height, width, slices_per_angle, num_angles] = size(data);

for angle = 1:num_angles

    % Extract the data for the current angle

    angle_data = data(:, :, :, angle);

    % Define the filename for the NIfTI file

     filename = sprintf('angle_%d.nii', angle);

    % Save the angle data as a NIfTI file

      niftiwrite(angle_data, filename);

    end

So, basically you will loop through each angle, extract the corresponding 3D slice, and save it as a NIfTI file using niftiwrite. The filenames will be then dynamically generated to reflect the angle number. Hope, you have a better solution.