Yeap I misunderstood, thanks Matt ;)
Stam
On 31 May 2011, at 15:45, Matt Glasser wrote:
> 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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