To use the stop masks, you will need to track symmetrically in two steps (the builtin option won’t work in this case).  Do the following Seed A à Target B + Stop B and then add this result with fslmaths to Seed B à Target A + Stop A.  Waypoint will work the same as Target in this case. 

 

I don’t know what SPM.mat is, is that a ROI file or something?  You would need to convert any ROI file to NIFTI, and then it would need to be in the correct space (either native diffusion space, or some other space for which you have specified a transformation matrix.


Peace,


Matt.

 

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mayuresh K
Sent: Wednesday, April 14, 2010 11:26 PM
To: [log in to unmask]
Subject: Re: [FSL] probtrackx question

 

Hi Matt,

 

Thanks for your prompt reply!

 

A followup on this - How can I run the "track symmetrically" option? 

 

Just to clarify, with the track symmetrically option, tracking will be done once starting from the seed to the target and then a second time from the target to the seed? How should I specify my termination and waypoint masks then?

 

Cheers,

Mayuresh

 

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shantanu ghosh
Sent: Wednesday, April 14, 2010 11:16 PM
To: [log in to unmask]
Subject: Re: [FSL] probtrackx question

 

As a follow up of this question, can we use output from SPM (ie spm.mat) as seed and target/stop masks in the gui?  what will be the command line code for that?

Thanks in advance,

Shantanu


 

+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-

P Please consider the environment before printing this e-mail

 

Shantanu Ghosh, PhD

Assistant Professor

Department of Humanities and Social Sciences

Indian Institute of Technology Delhi

Hauz Khas

New Delhi 110 016

INDIA

T +91.11.2659.1382

F +91.11.2659.2277

 

 

From: Matt Glasser <[log in to unmask]>
To: [log in to unmask]
Sent: Thu, 15 April, 2010 7:52:34 AM
Subject: Re: [FSL] probtrackx question

To get the pathway you want, specify a seed mask, a target mask, and the
same mask as a stop mask (same as the target).  The size of the masks might
make less of a difference than the fact that you will encounter a different
pattern in the diffusion vector fields tracking in one direction as tracking
in the other.  You might want to track symmetrically to avoid these
concerns.  You could exchange the seed and target+stop masks and then sum
the results.

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Mayuresh
Sent: Wednesday, April 14, 2010 9:17 PM
To: [log in to unmask]
Subject: [FSL] probtrackx question


Hello all,

I am running Probabilistic tracking in FSL 4.1.4 using a seed and target
mask approach with an interest in analyzing the fiber connections existing
"only between" the seed and target mask.
Basically I am want to get fiber tracts starting from the seed and
terminating in my target - excluding sections of the fibers going beyond the
seed mask or the target mask. How can I do this?

A second question - my seed (A) and targets (B) are of different sizes - so
would it matter if I tract from A to B instead of B to A?

Thanks,
Mayuresh.