I'm wondering if there is a way to automatically extract and save (in a .trk or .nii file) a specific tract based on one or more predefined masks (available in NIFTI format) and the results of a tractography such as with the FACT method.
I know how to do that manually in Trackvis, however, as I've a lot of subjects to process, I'm looking for an automatic method.
Unfortunately that is not feasible in TrackVis. However, I'm planning to include my old command-line based track_vis program in the next release. It has an option to do that.
The command-line version was an old program intended initially for in-house use only and has not been updated for a while. I need to do a little patch-up to make sure it works with the latest data format and such. I hope to release it in a month or so.
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