Hi


Sorry for not being more clear.  I was basically wondering if one could enter the .mat affine transforms when you click on the nonlinear toggle, and 'probtrackx2' automatically "finds" the associated warps files in the same directory.  I see from your reply that the *warp.nii.gz files are what you are actually supposed to enter in the GUI.  Is the affine component already "embedded" into the warp field?

Yes the affine is already part of the warp.


So, what does happen if you select the nonlinear toggle, but enter the .mat transforms?  In that case, 'probtrackx2' still completes, but I assume that it only uses the affine transforms between seed and diff space?

If you enter a .mat as the seed-to-diff transform, then this transform is used (as an affine) and the diff-to-seed transform is ignored. 
It you enter a .mat as the diff-to-seed transform, then you should get an error. 


Cheers
Saad



thanks,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: [log in to unmask]

From: Saad Jbabdi <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, February 5, 2013 5:02 PM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] probtrackx and non-linear transforms

Hi - Do you mean you used the GUI?  In which case, if you click on the nonlinear toggle, you should have the option of selecting both forward and inverse warps. This choice should be reflected in the probtrackx2 call that the GUI creates.  Is this not the case for you?

The probtrackx2 GUI does not search the directories for .mat or warp files, you have to provide them explicitly.

Cheers
Saad


On 5 Feb 2013, at 22:56, Michael Harms wrote:


Hi Saad,
I used "Fdt" to generate an example 'probtrackx2' command involving a seed mask that was non-linearly registered to "Seed space".
I noticed that the ensuing command only uses ".mat" files, and no "warp.nii.gz" files.

What tells 'probtrackx2' that you have a non-linear registration?  Is it the existence of the --invxfm argument itself?
And second, I'm guessing that 'probtrackx2' automatically searches the directory with the .mat files to locate the corresponding warp transforms?

thanks,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: [log in to unmask]

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)











--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)