Hi,
I'm afraid you can't use flirt within the scripts in this way as
currently it's matrix output format isn't compaible to use as input
to nreg in this way. So although you can use flirt to generate a
"standard-space" version of your target, _for use as the standard
space image "MNI152"_, you can't use it in conjunction with areg/nreg/
transformation.
Cheers, Steve.
On 28 Sep 2006, at 08:50, Stephen Rose wrote:
> Hi Steve
>
> Thanks for this information. I found (as you might expect)
> selection of the target FA map is critical for good registration.
> The mean FA maps and skeleton now look fine. Just for comparison I
> would like to try and run flirt in tbss_3 instead of the affine
> transformation, but I am not sure what lines of code to change (if
> any) in the following step.
>
> echo "affine-registering target to MNI152 space"
> ${D}/areg $M target.hdr -dofout target_to_MNI152.dof -parameter $
> {D}/affineCC.par
> ${D}/transformation target.hdr target_to_MNI152.hdr -dofin
> target_to_MNI152.dof -linear -target $M
>
> Any help would be much appreciated.
>
> Cheers
> Stephen
>
>
>
> On 27/09/2006, at 6:24 PM, Steve Smith wrote:
>
>> Hi - I'm not sure what you mean by "unusual distortions" - I'm
>> guessing that you're just referring to the fact that the target
>> image is being upsampled to 1mm for use as the "standard space",
>> but it it's primary intrinsic directions aren't aligned with the
>> image matrix axes. You might be able to solve this by using flirt
>> to align the target image to mni152 (with 1mm output) and use that
>> as the target instead - hopefully that should work ok (flirt is
>> more robust than the affine transformation used in tbss_3).
>>
>> Cheers, Steve.
>>
>>
>>
>> On 27 Sep 2006, at 08:24, Stephen Rose wrote:
>>
>>> Hi
>>>
>>> I am trying to analyse some preterm neonate DTI data using TBSS.
>>> I seem to be running into
>>> problems with tbss_3_postreg, with registration of my neonate
>>> brain FA maps to mni152 space.
>>> My thoughts are that it would more appropriate to complete the
>>> entire analysis in raw image space
>>> (eg target FA map) rather than forcing registrations into 152 space.
>>>
>>> In a previous query by someone else it was suggested to change:
>>>
>>> $FSLDIR/bin/flirt -in $FSLDIR/etc/standard/avg152T1_brain -ref
>>> $FSLDIR/etc/standard/avg152T1
>>> -out MNI152 -applyisoxfm 1
>>>
>>> to
>>>
>>> $FSLDIR/bin/flirt -in target -ref target -out MNI152 -applyisoxfm 1
>>>
>>> I have tried this option but get unusual distortions on the
>>> target_to_MNI152 and FA skeleton maps
>>> (see attached files).
>>>
>>> Is there a way to bypass the registration step to 152 space (in
>>> tbss-3-postreg) and keep
>>> everything in the target image space for the remainder of the
>>> analysis steps? This seems the only
>>> option until someone comes up with a neonate equivalent of the
>>> mni152. Any help would be much
>>> appreciated.
>>>
>>> <skeleton.jpg>
>>> <target.jpg>
>>
>>
>> ---------------------------------------------------------------------
>> ------
>> 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
>> ---------------------------------------------------------------------
>> ------
>>
>>
>
> Dr. Stephen Rose
> Senior Research Fellow
> Centre for Magnetic Resonance
> University of Queensland
> Brisbane, QLD, 4072 Australia
> Telephone: +61 7 32327480
> Mobile: 0412023958
> Fax: +61 7 33653833
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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)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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