Hi,
That's right - if you use standard2str.mat (not standard2diff.mat as you put first)
and the anatomical image as the reference (like you have in your flirt command)
then that will work fine.
The reference image is any image in the desired output "space", and determines
the Field Of View (FOV) and the voxel size.
All the best,
Mark
On 31 May 2011, at 18:05, Leslie Engineering wrote:
> Right, so back to the original question :) (i'm sorry my terminology must be poor).
>
> If I decide I want everything to be in structural space, can I transform my standard space masks by using the standard2diff and the BETed anatomical as the ref?
>
> i.e.
>
> flirt -in mask -out mask2str -ref anat_BET -applyxfm -init standard2str.mat
>
> ... i guess I don't understand what images are chosen for the reference (-ref). Is it any image from that space in order to have a volume association?
>
> thanks and sooooo sorry
>
> On Tue, May 31, 2011 at 12:53 PM, Matt Glasser <[log in to unmask]> wrote:
> You are only allowed to specify one transform that transforms all the masks, so you are correct that you need to have them all in the same space. I would recommend deciding what space you want your results in and then transforming all masks in to that space.
>
>
> Peace,
>
>
> Matt.
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Leslie Engineering
> Sent: Tuesday, May 31, 2011 11:35 AM
>
>
> To: [log in to unmask]
> Subject: Re: [FSL] question
>
>
> In other words, my seed mask and my waypoint masks are in different spaces (standard and structural).
>
> So I believe I would need to transform them before running the probtrack
>
> On Tue, May 31, 2011 at 12:21 PM, Leslie Engineering <[log in to unmask]> wrote:
>
> Thanks. Just to clarify, in the probtrackx panel it asks whether I want to transform the seed mask, but I have waypoint masks, and it doesn't offer the same transformation.
>
> So if i were to do it manually, I know i use the transforms from the xfm folder (i.e. standard2diff or str2diff), but what do I use as the reference image... or it is not necessary to have one??
>
> Thanks and sorry. I just started using fsl a couple weeks ago.
>
> Leslie
>
>
> On Tue, May 31, 2011 at 11:08 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:
>
> 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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