Hello,

Does anyone know if there is any information on the size, shape, and exact locations (MNI coordinates) of the ROI's in atlas.nii file within conn. I have tried to separate the ROIs in this image into different files, but I have been unsuccessful. There is a .mat file within the results/firstlevel/([specific analysis] folder that contains a variable xyz that gives MNI coordinates for each ROI. Plotting these points gives a region that appears to be the center of the ROI. Can anyone confirm this?

Thank you in advance for your help!

Best,

Greg

There are some information in the directory where you install(unzip) conn.

In my case,
~/conn/rois/  is my conn installation directory.
If you look at this directory, you may see several files such as text, images and NIFTi files regarding atlas and networks which CONN uses.
For example, if you open 'atlas.info' file you can see the rules that CONN used to define ROI.
(Because I'm using linux, 'cat' command works, but I don't know in MAC...)

As written in this file, CONN uses the Harvard-Oxford Atlas for both cortical and subcortical atlas.
For more information, you have to read 'atlas.info' file because there are reference paper.
That paper would give more information I think.

Good luck for your research!

Hi,

Yes, the xyz variable contains the centroid of each of the ROIs.

If the atlas file is 4D, you can try SPM's 4D to 3D utility to quickly get to separate ROI files. In either case, this can be achieved using something on the lines of:

%% This case is for 3D atlas file having unique intensity values for each ROI
% Read in atlas.nii file
vol_atlas   = spm_vol('atlas.nii');
data_atlas = spm_read_vols(vol_atlas);
data_tmp  = data_atlas;

% Get all unique intensities
roi_vals    = unique(data_atlas);
num_vals = length(roi_vals);

% Loop over each intensity
for i = 1:num_vals

% Binarize the values
data_tmp(data_tmp~=roi_vals(i)) = 0;
data_tmp(data_tmp==roi_vals(i)) = 1;

% Write out
roi_name = ['ROI_', num2str(i, '%03d'), '.nii'];
vol_atlas.fname = roi_name;
spm_write_vol(vol_atlas, data_tmp);

% Reassign original values to data_tmp
data_tmp = data_atlas;
end

% ----------------------------------------------------------------------

%% This is the case of 4D atlas file where each volume is an ROI
% Read in atlas.nii file
vol_atlas = spm_vol('atlas.nii');
data_atlas = spm_read_vols(vol_atlas);

% Get number of ROIs
num_rois = size(data_atlas,4);

% Loop over each volume and write it out
for i = 1:num_rois
roi_name  = ['ROI_', num2str(i, '%03d'), '.nii'];
vol_atlas(i).fname = roi_name;

% If a field n exists, set it to 1
if isfield(vol_atlas, 'n')
vol_atlas(i).n = [1,1];
end

spm_write_vol(vol_atlas(i), squeeze(data_atlas(:,:,:,i)));
end


As an additional note, it is worthwhile to change the data type (vol.dt) as all ROIs from above are binary. Also the .info file contains a lot of useful information. The dimension of the overall file can be picked up from the NIfTI header.


Hope this helps


Best
Pravesh


Originally posted by Hyunwoo Kim: