Hi
If you have a single NIFTI mask with one integer value per ROI, you can easily split that into multiple different ROIs using FSL tools.
E.g. the command below
fslmaths <volume_with_all_rois> -thr <val> -uthr <val> -bin <output_mask>
will output a mask of the ROI with label =<val>
So you can just loop over all the possible values to create multiple masks.
Of course you can also use python or matlab to split your masks.
Cheers
Saad
> On 19 Mar 2020, at 16:27, Czime Lit <[log in to unmask]> wrote:
>
> Hello,
>
> I am trying to run probtrackX with the --network flag and with an alternative set of atlases (i.e. not traditionally supplied with fsl, but obtained from other sources such as gihub or nitrc). I am having a problem that these atlases are defined as single volumes with a number of values, each value defining an roi. They often have something like a text file with unit number, name and XYZ coordinates, or with a set of RGB values instead of the coordinates. How can I split them up to make them suitable for the roi-roi tractography?
>
> Many thanks!
>
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