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Subject:

Re: Coregistration and normalisation

From:

Simone Reinders <[log in to unmask]>

Reply-To:

Simone Reinders <[log in to unmask]>

Date:

Tue, 22 Apr 2008 11:27:39 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (60 lines)

Dear Vivien Tsen,

I can follow your first part of your email and agree on 1. and 2.
However, when it comes to your question it is not clear to me what you
want. Especially the part of combining EPI and unified segmentation
does not  make sense to me.

However, perhaps these considerations help you:
- Co-register EPI and T1 and check using the 'check reg' option if
this was successful. In your case this check seems important as you
doubt that the quality of your EPI is good enough for a successful
registration.
- After co-registering your EPI and T1 images you can normalize your
subject specific T1 to the MNI template. This will give you subject
specific normalisation parameters with which you can normalize (write)
your EPI images, because they are in the same orientation due to the
co-registration. In theory this will correctly normalise your EPI
scan, the only question is what are you normalising when you have that
many artifacts...
- If your EPI images have that much distortion you should wonder about
the reliability and usability of your EPI data...
- T1 sequences are usually much less affected by susceptibility
artifacts than EPI. Do check your T1 images. As structural
segmentation is independent of EPI you can always do VBM analysis if
the quality of your T1 is good, i.e. no need to co-register EPI and
T1.

I hope this helps even though I did not understand your question.

Kind regards,
  Simone.

---
Dr. A.A.T.Simone Reinders, MSc PhD
King's College London
Institute of Psychiatry (IoP)
Box P063, De Crespigny Park
London SE5 8AF
United Kingdom

On Tue, Apr 22, 2008 at 12:38 AM, Vivien Tsen <[log in to unmask]> wrote:
> Based on previous posts, the advantage of using structural (T1-weighted)
>  image for co-registration and spatial-normalization as opposed to
>  normalizing functional images directly to the EPI template is that:
>     1. T1-weighted images have higher spatial resolution which should allow
>  better overlap with the corresponding structures in the template.
>     2. there is the issue of EPI distortion variability in subjects and
>  that of the template (which would be less of an issue in structurals).
>
>  My question is:
>  if the EPI images are prone to distortion, it is quite likely that the
>  functional image (EPI) and the structural image (T1-weighted) cannot be
>  matched by rigid-body transformation (realignment or co-registration)
>  alone. So, if the EPI cannot be well-matched with the structural, how much
>  of an advantage is it using the T1-weighted for unified segmentation after
>  co-registration? Has a comparison been published between the two methods?
>
>  Thanks.
>

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