So if I'm understanding this right, you have:
1) Native T1 image: T1
2) Segmented native T1 image: c1T1
3) Mean EPI aligned with native T1 image (NOT imported T1) and c1T1:
EPImean
4) Imported T1 segments: rc1T1
What you want is meanEPI in the same space as the r1c1T1 image.
Then it's easy. Do a coreg with this setup:
Source: c1T1
Ref: rc1T1
Other: meanEPI
c1 segment in native space coregisters to rc1 in imported space (should
be very very accurate) and drags the (already aligned) meanEPI with
it. Done =)
-Neil
kambiz rakhshan wrote:
> Dear Dana,
>
> Thanks for your reply but this is not actually what I am looking for.
> For some specific reason I need the EPI mean to be aligned with the
> imported T1 images *not the T1 image*. I do know that usually people
> coreg T1 image to Mean EPI and then compute the flow field from the
> imported segmented image (e.g. rc1) and then apply the computed flow
> field to both native c1T1 and mean EPI. In my case, I implemented a
> very sensitive supervised approach using DARTEL for longitudinal
> analysis and now I need to apply multiple of flow fields to
> corresponding EPI in order to do multimodal analysis.
>
> In short, all I need to do is to get EPI mean of fMRI and imported T1,
> aligned ! I guess, one can not coreg EPI mean and rc1 or c1 (do you
> think if coreg algorithm would be able to properly coregister mean EPI
> to c1?) but instead coreg EPI mean and rT1 (Again I emphesis that I do
> not want to coreg EPI mean and T1).
>
> Any help would be highly appreciated!
> Best
>
>
> Best
> Kambiz
>
> --- On *Wed, 4/7/10, Dana Perantie /<[log in to unmask]>/* wrote:
>
>
> From: Dana Perantie <[log in to unmask]>
> Subject: Re: importing Structural T1 images into DARTEL
> To: [log in to unmask]
> Date: Wednesday, April 7, 2010, 2:01 PM
>
> P.S. You can use “Create Warped” to apply the flow field to the
> T1. The function Create Warped recognizes whether the image is
> already procrustes aligned, so it may apply to r* or native
> images. Otherwise, the flow field applies to the native space images.
>
>
>
>
>
> *From:* SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] *On Behalf Of *Dana Perantie
> *Sent:* Wednesday, April 07, 2010 1:50 PM
> *To:* [log in to unmask]
> *Subject:* Re: [SPM] importing Structural T1 images into DARTEL
>
>
>
> Hi Kambiz,
>
> If you have already calculated the DARTEL flow, you can apply it to
> the T1 image in native space – you can apply it to the image where the
> segment came from.
>
> Or were you asking if you can run DARTEL on a whole brain image? I
> don’t know about that…
>
> -Dana
>
>
>
>
>
> *From:* SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] *On Behalf Of *kambiz rakhshan
> *Sent:* Wednesday, April 07, 2010 11:25 AM
> *To:* [log in to unmask]
> *Subject:* [SPM] importing Structural T1 images into DARTEL
>
>
>
> Dear Dartel Experts,
>
>
>
> For some specific reason, I do need to import a T1 image, not the
> segmented one c1T1, into DARTEL space. Is there any easy way of doing
> this?
>
> many thanks!
>
>
>
> kambiz
>
>
>
>
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