How to Get Grey Matter Volume of Specific Brain Regions in SPM/MATLAB?

Question

Arjun 2024-2-11

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https://ww2.mathworks.cn/matlabcentral/answers/2080931-how-to-get-grey-matter-volume-of-specific-brain-regions-in-spm-matlab

评论： Arjun 2024-3-25

I want to extract grey matter volume for specific regions (e.g., prefrontal cortex, amygdala) from MRI data that has been preprocessed. My lab gave me a code (see below) for calculating global grey matter volume (and white matter volume and CSF), but I am not sure whether I can adapt this script to also extract regional grey matter volume. Would appreciate help!

% Get total volumes in mm3

grey_totals(i) = get_totals ([data_path num2str(subnum) '/c1' num2str(subnum) '.nii']);

white_totals(i) = get_totals ([data_path num2str(subnum) '/c2' num2str(subnum) '.nii']);

csf_totals(i) = get_totals ([data_path num2str(subnum) '/c3' num2str(subnum) '.nii']);

end

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Arjun 2024-2-13

在 MATLAB Online 中打开

In general, you might not be running MATLAB from the folder where you have your data, so you'd need something like:

amygdala_totals = get_totals('/path/to/my/data/Amygdala_mask.nii');

With reference to the comment above, I am currently running the code:

%% get amygdala grey, white matter, and CSF volumes
%get SPM12
addpath '/Users/arjunthanaraju/Downloads/PhD/spm12/';
spm
for i = 1:length(files_mri)
subnum = files_mri(i).name; %get names of each subject's folder
%add amygdala mask to get_totals function
amygdala_totals = get_totals(['/Volumes/SEAGATE_BAC/Amygdala_Mask.nii']);
%get amygdala volumes in mm3
amygdala_grey_totals(i) = amygdala_totals (['/Volumes/SEAGATE_BAC/397Participants/'  num2str(subnum) '/c1' num2str(subnum) '.nii']);
amygdala_white_totals(i) = amygdala_totals (['/Volumes/SEAGATE_BAC/397Participants/'  num2str(subnum) '/c2' num2str(subnum) '.nii']);
amygdala_csf_totals(i) = amygdala_totals (['/Volumes/SEAGATE_BAC/397Participants/'  num2str(subnum) '/c3' num2str(subnum) '.nii']);
end 
%combine into table
globals = table(subjects.subjects, amygdala_grey_totals', amygdala_white_totals', amygdala_csf_totals');
%convert Var1 column name to Subjects
globals.Properties.VariableNames{'Var1'} = 'Subjects';

When I run this code, I get the previously stated error:

Index exceeds the number of array elements. Index must not exceed 1.

Can you point me towards where I made a mistake in the code above? Thank you so much!

Karl 2024-2-14

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Excellent! A possible next step would be to organise the ROI masks for which you want to extract volume information in a way that makes them easy to analyse.

In the example code that you have, there's a folder for each subject, and each subject folder contains multiple ROI masks. You could do something similar. For example, if the first subject has identifier 12345, you could create a folder /Volumes/SEAGATE_BAC/397Participants/12345, and inside that place the ROI masks, for example amygdala_12345.nii, some_other_roi_12345.nii.

You could then loop over subjects, extracting volumes for each ROI. If in your code:

subnum = files_mri(i).name;

correctly defines the subject identifier, you should be able to obtain volumes with lines like:

amygdala_totals(i) = get_totals(['/Volumes/SEAGATE_BAC/397Participants/'  num2str(subnum) '/amygdala_' num2str(subnum) '.nii']);
some_other_roi_totals(i) = get_totals(['/Volumes/SEAGATE_BAC/397Participants/'  num2str(subnum) '/some_other_roi_' num2str(subnum) '.nii']);

You'd then change the definition of the globals table to reflect the ROIs for which you have data.

Karl 2024-2-19

You're welcome! If you're unable to get the looping to work, please do submit another question, ideally including code and files for reproducing the problem (as you did in the comments here). Hopefully I, or someone else, will be able to help!

Arjun 2024-2-20

Thank you so much! I definitely will.

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Answer 1

Karl 2024-2-18

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2080931-how-to-get-grey-matter-volume-of-specific-brain-regions-in-spm-matlab#answer_1411228

在 MATLAB Online 中打开

Summarising from the comments, if 'roi.nii' is a NIfTI file containing a binary mask representing a region of interest (ROI), and the Statistical Parametric Mapping (SPM12) package is on the MATLAB path, the ROI volume can be calculated using the get_totals() function written by Ged Ridgway:

% Calculate ROI volume using SPM12.
roi_volume = get_totals('roi.nii');

The ROI volume can also be calculated without having SPM12 installed:

% Write example ROI (cuboid) in NIfTI format.
mask = zeros(100,100,100);
[x1, y1, z1] = deal(31, 41, 11);
[dx, dy, dz] = deal(40, 20, 80);
mask(x1:x1+dx-1,y1:y1+dy-1,z1:z1+dz-1) = 1;
niftiwrite(mask,'roi.nii')
% Read ROI from NIfTI file, and calculate its volume.
roi_info = niftiinfo('roi.nii');
roi = niftiread(roi_info);
roi_volume = sum(roi(:)) * prod(roi_info.PixelDimensions)
roi_volume = 64000
% Check that the calculated volume is as expected from the cuboid dimensions.
assert(roi_volume == dx * dy * dz)

Whichever method is used, the volume units should be checked.

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Arjun 2024-3-25

Just wanted to add on for future users that the CAT12 toolbox in SPM also provides estimates for each ROI based on selected atlases. This made it very easy for me to extract ROI values for both grey matter volume and cortical thickness!

You can read more in the CAT12 manual available here: https://neuro-jena.github.io/cat12-help/

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