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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
>