Hi Eugene,
Thanks. Let me see if I've understood this properly.
T1.nii (1mm isotropic)
EPI_A.nii (3mm isotropic)
EPI_B.nii (3mm isotropic - coregistered with EPI_A, but 4D)
We want to coregister the EPI to the T1 (ignore the problems of doing
this for the moment). So we run flirt to get the transformation
matrix:
flirt -in EPI_A.nii -ref T1.nii -omat register.mat
We now want to transform EPI_B such that it is coregistered with the
T1, but the voxel sizes remain as 3mm isotropic. Do we do the
following?
applyxfm4D EPI_B.nii EPI_A.nii EPI_B_trans.nii register.mat -singlematrix
This should give me EPI_B coregistered with T1, but with the voxel
resolutions of EPI_A. Is that correct?
Cheers,
Satra
On Fri, Mar 20, 2009 at 11:54 AM, Eugene Duff <[log in to unmask]> wrote:
> Hi Satra,
>
> The output voxel size is determined by the refvol you provide with the -ref
> option in flirt. This can be different from the target image used when the
> transformation was calculated. So you just need to use a refvol image with
> the image properties you desire.
>
> Hope that helps.
>
> Eugene
>
>
>
> 2009/3/20 Satrajit Ghosh <[log in to unmask]>
>>
>> I have a registration file that registers a functional image (3mm
>> isotropic) to a structural image (1mm isotropic). Is there a way to
>> use applyxfm4d or another tool such that when I transform the
>> functional images, I can specify the voxel resolution of the
>> transformed volume?
>>
>> Thanks,
>>
>> Satra
>>
>>
>> On Fri, Mar 20, 2009 at 11:21 AM, Mahinda Yogarajah
>> <[log in to unmask]> wrote:
>> > Dear FSL Users,
>> >
>> > Is there an option in FNIRT normalisation equivalent to the preserve
>> > concentrations option in SPM5 when one writes out normalised images ?
>> >
>> > Thanks.
>> >
>> > Mahinda
>> >
>
>
>
> --
>
> Eugene Duff
>
> FMRIB Centre,
> University of Oxford
> John Radcliffe Hospital, Headington OX3 9DU Oxford UK
>
> Ph: +44 (0) 1865 222 739 Fax: +44 (0) 1865 222 717
>
> --
>
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