Hi all,
The size of the connectome matrix is 84 x 84, which means 84 regions are there. If I want fewer regions then what will be the process.


A matrix that is smaller than 84x84. For example if you have only 2 rois in the node image are given, then the connectome matrix will be 2x2. Hope this answers what you were asking.

Thanks. But how to change the number of ROIs in node image. As I am new in this, I don’t know how to change ROIs.

A parcellation image is simply an image with integer values, and any non-zero value is interpreted as the index of the corresponding ROI. So if you need fewer ROIs, you need to provide an image with fewer unique non-zero values in it – and preferably also with a correspondingly smaller maximum value, since that will also reduce the size of the connectivity matrix produced (otherwise, absent indices still generate a row/column in the matrix, even though they will be zero). See here for further insights.

To do this manually will I guess be fiddly. You don’t need to use MRtrix tools for this though, as long as you can provide a suitable parcellation image in NIfTI or mif format (or any other supported format).

However, given what it looks like you’re trying to do, the obvious command to use here is labelconvert – especially if you already have an existing parcellation, and you just need to reduce the number of nodes. You’d need to generate your own lookup table, but that shouldn’t be too onerous (and certainly easier than modifying the image itself directly…).