1) Update to the latest version of FSL 4.1.4 and see if you still have this
issue.
2) --mesh is used for tracking from a FreeSurfer surface and label file, but
it is not currently working correctly yet. --os2t is for seeds to targets
mode. You use this if you want to count how many times samples from your
seed voxels reach a particular list of target ROIs. You can use this to
compare connection probabilities between targets, and do stuff like
segmenting the thalamus.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Conrad Rockel
Sent: Wednesday, August 05, 2009 3:12 PM
To: [log in to unmask]
Subject: [FSL] behind in my patches? (probtrackx)
Hi FSL!
A couple of questions regarding probtrackx, and for the record, I am running
v4.1.2.
1) I have been running some tracts, and think I that I have encountered
some problems that were addressed a while ago in this forum. I have been
trying to use a seedmask, 2 waypoint masks, and then a termination mask, or
alternatively, an exclusion mask. It seems as though the tract in question
only stops a voxel or two PAST the termination mask. When I use the
exclusion mask, it doesn't seem to be excluding, but merely terminating the
tract in question. I think that there was a patch that was released a while
ago to address this, but I can no longer find it on your site. Do I have to
update the full FSL to fix this problem?
2) While investigating the probtrackx command-line, I noticed a couple of
options: --mesh and --os2t. I was wondering how these are to be used, since
they appear not to be available when using the GUI. I tried to incorporate
them from command-line, the former to experiment with 3D Viewer, and the
latter in an attempt to fix problem (1). Both attempts failed miserably
because I didn't supply some sort of other info, so was just curious as to
how these are used.
Cheers,
Conrad
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