Stam,
I think she wants to take the mask into diffusion space.
The best way to do that is to use the --xfm option in probtrackx to specify
the transform internally.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Stamatios Sotiropoulos
Sent: Tuesday, May 31, 2011 9:33 AM
To: [log in to unmask]
Subject: Re: [FSL] question
Hi,
you need to specify the standard space image, e.g.
$FSLDIR/data/standard/MNI152_T1_2mm.
Cheers,
Stam
On 31 May 2011, at 15:01, Leslie Engineering wrote:
> If i have a mask in standard space that I would like to use as a waypoint
in probabillistic tracking, how do I properly transform to diff space. I
know the transform mat files are in bedpost/xfm but what do i use as a
reference file??
>
> i.e. flirt -in mask.niigz -out mask2diff -ref ?? -applyxfm -init
.../bedpost/xfm/standard2diff
>
>
> thanks
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