HI - have a look inside the dof2warp and tbss_deproject scripts to
find out about warp field inversion. If you've used FSL4 then you
should have what you need.
Cheers.
On 20 Sep 2007, at 14:51, Dr. Carol Docherty wrote:
> Dear Gwenaelle,
>
> I ran the steps you outlined below to non-linearly register my T1w-
> image to MNI space using FSL. Is it now possible to determine and
> apply the inverse of this matrix to the MNI template, so as to have
> the template in subject space? How might you suggest doing this?
>
> Thanks in advance,
>
> Carol
>
> ----- Original Message -----
> From: "Gwenaëlle DOUAUD" <[log in to unmask]>
> To: [log in to unmask]
> Sent: Wednesday, September 12, 2007 9:07:07 PM (GMT+0100) Europe/
> Berlin
> Subject: [FSL] RE : [FSL] Non-linear registration to MNI space
>
> Dear Carol,
>
> given your T1-w image in the correct analyze format
> (you need to use tbss_1_preproc, see tbss or fsl-vbm
> pages) and BETted: yourT1.hdr
>
> and your brain template in the same format (probably
> ~fsl/etc/standard/MNI152_T1_1mm_brain.nii.gz or 2mm):
> yourMNItemplate.hdr,
>
> you need first to determine the affine parameters of
> the transformation from your T1-w to the MNI template:
>
> ~fsl/bin/DR/areg yourMNItemplate.hdr yourT1.hdr
> -dofout yourT1_aff.dof -parameter
> ~fsl/bin/DR/affineCC.par
>
> then the non-linear parameters based on the affine
> ones:
>
> ~fsl/bin/DR/nreg yourMNItemplate.hdr yourT1.hdr -dofin
> yourT1_aff.dof -dofout yourT1_nl.dof -ds 20 -Tp 0
> -parameter ~fsl/bin/DR/nonlinearCC.par
>
> and finally to apply the non-linear parameters to your
> T1-w image:
>
> ~fsl/bin/DR/transformation yourT1.hdr
> yourT1_normalised.hdr -dofin yourT1_nl.dof -linear
> -target yourMNItemplate.hdr
>
> Hoe this helps,
> Gwenaelle
>
>
> --- "Dr. Carol Docherty" <[log in to unmask]> a écrit
> :
>
>> Hi,
>>
>> I am trying to register a T1 weighted dataset to MNI
>> space using the non-linear registration option in
>> TBSS (I read it was possible from a previous mail on
>> the list). However, I am not entirely sure of the
>> steps I should follow to do this, and would
>> appreciate it if someone on the list could perhaps
>> explain it some more.
>>
>> Thanks in advance,
>>
>> Carol
>> --
>> Dr Carol Docherty
>> Postdoctoral MRI Scientist
>> Department of Neurophysics
>> Max-Planck Institute for Human Cognitive and Brain
>> Sciences
>> Stephanstraße 1A
>> 04103 Leipzig
>> Germany
>>
>> Tel: +49 (0)341 99 40 291
>> Fax: +49 (0)341 99 40 221
>> Email: [log in to unmask]
>>
>
>
>
>
> ______________________________________________________________________
> _______
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>
>
> --
> Dr Carol Docherty
> Postdoctoral MRI Scientist
> Department of Neurophysics
> Max-Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A
> 04103 Leipzig
> Germany
>
> Tel: +49 (0)341 99 40 291
> Fax: +49 (0)341 99 40 221
> Email: [log in to unmask]
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
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