1) Yes that is fine to do. The purpose of thresholding is to exclude low
probability results that are not of interest and to highlight higher
probability results that are of interest. Exactly what the right threshold
for any given pathway and the right method of thresholding has been much
discussed on the list. As long as your thresholding accomplishes the basic
objective above, however, it is okay.
2) Classification results are very different from fdt_paths results. You
will need to specify some classification targets, and then will get images
of your seed mask that contain the number of samples in each seed voxel that
reached the target. If you want other things like terminations and
waypoints, you will still need to specify them.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Torsten Ruest
Sent: Wednesday, June 02, 2010 1:29 PM
To: [log in to unmask]
Subject: [FSL] probtrackx options
Hi there,
I have some simple questions regarding probtrackx options, I am sure have
been asked before however I couldn't find them in the archives.
1.) For training purposes, I used a unilateral BA4 mask (motor cortex) as
seed mask, and selected as waypoint and termination mask a medulla mask to
get the cortico-spinal tract. The fdt_paths result looks a bit messy,
however if I threshold at 50 it looks quite nice. I think that's Ok to do
as I remove low probability voxels. Is this right?
2.) What would the settings be if wanted to use the classification option,
and fdt_paths should look the same as in 1.), ie. would I need to specify
the termination and waypoint masks as above?
I hope these questions make sense.
Thanks for any input.
Cheers,
Torsten
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