Indeed - however the FIRST models (that presumably you then want to
use after the initial flirting stage of FIRST) may be requiring that
the standard-space version of the image is at 1x1x1mm. Brian, is that
the case?
Cheers.
On 29 Jan 2009, at 06:44, wolf zinke wrote:
> Hi Mark,
>
> You might modify the script (/usr/local/fsl/bin/first_flirt) to
> achieve this. In line 130 there is a final flirt call to apply the
> transformation:
> ${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${FSLDIR}/data/standard/$
> {refim} -applyxfm -init ${B}_cort.mat
>
> If you change it to
> ${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${A} -applyxfm -init $
> {B}_cort.mat
>
> I guess this could do the trick. Another option might be to change
> the reference image (line 90: refim=MNI152_T1_1mm) and use one that
> you created for your purpose. However, you still might notice a
> degradation of the image quality that is due to the interpolation
> (add '-interp sinc' to the last flirt call to whether it improves).
>
> good luck,
> wolf
>
> Mark Schira wrote:
>> Hi
>> I ma trying to use the first_flirt script to rotate anatomy scans
>> into a
>> standard space.
>> first_flirt seems to do the job, however it also resizes the images
>> into a
>> standard resolution of 1x1x1 mm, thereby significantly reducing the
>> quality
>> of the data, which is in 0.75mm. (The reduction of quality is
>> rather dramatic!).
>>
>> So in other words I want to do exactly what first_flirt does, but
>> without
>> resizing to 1mm, but instead simply applying a rotation and
>> translation.
>> I looked hard but I couldn't identify an option for this, nor could
>> I see
>> where in the first_flirt script i would have to make the changes...
>> Cheers
>> M.
>>
>
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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)
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