You should always choose the best image as the target when flirting.
Cheers.
On 14 Aug 2007, at 08:09, Cherif Sahyoun wrote:
> Hi,
>
> Out of interest, as I was reading this: is it always a better idea to
> flirt from lower to higher res and then inverse the matrix? would
> flirting from standard to diff not work as well? or is it just so that
> you can more easily check the registration that way?
>
> thx,
> cherif
>
> On 8/14/07, Matt <[log in to unmask]> wrote:
>> You need to make a transformation matrix that describes the
>> transformation
>> from standard to diffusion space. Probably the best way to do
>> that is to
>> coregister your DTI b0 to standard space:
>>
>> flirt -in <b0File> -ref <standardFile> -omat <diff2standard.mat> -out
>> <b0File2StandardFile>
>>
>> Then verify that your coregistration was good by loading the
>> <b0File2StandardFile> on top of the <standardFile> in FSLView.
>>
>> Then invert the matrix so you have one that does the
>> transformation you
>> want:
>>
>> convert_xfm -omat <standard2diff.mat> -inverse <diff2standard.mat>
>>
>> Then you can apply the transformation matrix to your ROI, as you
>> describe
>> below.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>> On Behalf
>> Of David Roalf
>> Sent: Monday, August 13, 2007 5:43 PM
>> To: [log in to unmask]
>> Subject: [FSL] Coverting Standard Mask back to native space
>>
>> I would like to take a mask created in standard (MNI) space and
>> transform it
>> to native space using a b0 (DTI) image (NIFTI_gz file format). The
>> FSL FAQ
>> recommends using the following to covert a mask from one space to
>> another:
>>
>>>> flirt -in standard_mask -ref highres -applyxfm -init
>> standard2highres.mat -datatype float -out highres_mask
>>
>> then:
>> avwmaths highres_mask -thr 0.5 -bin highres_mask
>>
>> I have tried this command and I am prompted with the error: Could
>> not open
>> matrix file standard2highres.mat (and sure enough I don't have the
>> tool in
>> my usr/fsl/local/bin folder, but I do have std2imgcoord). So I am
>> unsure if
>> I simply do not have this correct tool or if I am doing something
>> incorrectly. I am running FSL 3.3 via Cygwin.
>>
>> D. Roalf
>> Oregon Health Science University
>> Portland OR
>>
>
>
> --
> ----------------------------------------------------------------------
> --------------------
> Cherif P. Sahyoun HST-
> MEMP
>
> Developmental Neuroimaging of Cognitive Functions
>
> C: 617 688 8048
> H: 617 424 6956
> [log in to unmask]
>
> "Live as if this were your last day. Learn as if you'll live forever"
> Ghandi
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> ---------------------
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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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