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help > RE: Combining Seeds
Dec 6, 2016 04:12 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Combining Seeds
Hi Humza,
Unless I understood your question incorrectly, you could just add different ROI mask files together to create one single ROI file. You can read them into MATLAB and do it, or just use 'imcalc' utility of SPM to read all masks together, and add them.
If you are referring to atlas files with different intensities for different ROI and you just want to select a sub-set of these ROIs you could do the following:
In case of probabilistic atlases, you would want to introduce an additional thresholding line above.
Hope the above helps.
Best
Pravesh
Originally posted by Humza Ahmed:
Unless I understood your question incorrectly, you could just add different ROI mask files together to create one single ROI file. You can read them into MATLAB and do it, or just use 'imcalc' utility of SPM to read all masks together, and add them.
If you are referring to atlas files with different intensities for different ROI and you just want to select a sub-set of these ROIs you could do the following:
vol = spm_read('atlas.nii'); % The
atlas file which you want to read from
vol_data = spm_read_vols(vol);
intensities = [10 20 30]; %
The intensities which you want to convert to ROI
dummy_mat = zeros(size(vol_data);
for i = 1:length(intensities)
tmp = vol_data==intensities(i);
dummy_mat = dummy_mat + tmp;
end
vol.fname = 'modified_atlas.nii'; % The
name of the new nifti file which you want to write
spm_write_vol(vol, dummy_mat);
In case of probabilistic atlases, you would want to introduce an additional thresholding line above.
Hope the above helps.
Best
Pravesh
Originally posted by Humza Ahmed:
Hello All,
I am wanting to conduct some ROI-ROI, and seed-voxel analysis using the default ROI's within the CONN toolbox. I am a bit confused about how to combine multiple ROI's or to use an entire network (as defined in CONN17a) as a single seed to use during first/second level analysis. Thanks for any guidance.
From,
Humza Ahmed
I am wanting to conduct some ROI-ROI, and seed-voxel analysis using the default ROI's within the CONN toolbox. I am a bit confused about how to combine multiple ROI's or to use an entire network (as defined in CONN17a) as a single seed to use during first/second level analysis. Thanks for any guidance.
From,
Humza Ahmed
Threaded View
Title | Author | Date |
---|---|---|
Humza Ahmed | Dec 6, 2016 | |
Pravesh Parekh | Dec 6, 2016 | |
mscahart | Jan 13, 2020 | |
Humza Ahmed | Jan 14, 2020 | |
mscahart | Jan 16, 2020 | |
Humza Ahmed | Dec 6, 2016 | |
Pravesh Parekh | Dec 6, 2016 | |