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FSL  July 2007

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Subject:

Re: Standard space mapping with flirt

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 26 Jul 2007 10:20:04 +0100

Content-Type:

text/plain

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text/plain (130 lines)

Hi - I would not use the 5th dimension as this is not yet fully  
supported in most implementations of NIFTI - I would find a  
workaround for that and re-test.

Cheers.

On 26 Jul 2007, at 11:11, Alle Meije Wink wrote:

> Hi -thanks for the quick reply!
>
> What I saw (with linear interpolation earlier, I thought sinc would be
> better for the real analysis) was that also took very long. I thought
> that something was happening outside just resampling.
>
> In the analysis there are some 4D files of 10 volumes -actually  
> they are
> 5D, because they are not time series so we put everything in dim[5]-
> which are in <double> format. So they are quite big...
>
> But then, I assume that files are resampled on a 3D (volume by volume)
> basis? Why would it be necessary then to load the whole series of  
> volume
> into the memory?
>
> My computer has 2 G of memory, so 91*109*91*8*10 = 72210320 = 69 M
> should not be a problem?
>
> I'll have another test with trilinear interpolation to see what that
> does to the speed. I'm afraid about what it will do to the quality  
> though...
>
> I have written B-spline interpolation code before (whose interpolants
> for degrees >2 are almost sinc functions) and that didn't seem to  
> suffer
> from increasing the degree that much. Are you sure this is what  
> makes it
> so slow?
>
> Thanks!
> Alle Meije
>
> Steve Smith wrote:
>> Hi - I would have expected changing the interpolation to have a large
>> effect. It is possible instead that applying flirt to the 4D  
>> dataset is
>> slow because doing that all in one is requiring too much RAM and your
>> computer is doing lots of swapping - in which case I would recommend
>> using avwsplit to split it down to 3D files, applying the  
>> transform with
>> flirt, and then recombining with avwmerge.
>>
>> Cheers.
>
>> On 26 Jul 2007, at 10:41, Alle Meije Wink wrote:
>>> Hi,
>>>
>>> I am using flirt for standard space mapping in my analyses. The  
>>> way I
>>> have set it up is as follows:
>>>
>>> All single-subject time series (4D) are in NifTI format, the time  
>>> series
>>> averages (3D) are called *NatAverage.nii, and the statistic  
>>> images (in
>>> native space) are all called Nat*.nii.
>>>
>>> I align the *NatAverage.nii file to the template $TEMPL (which in  
>>> this
>>> case is EPI.nii) and then use that transformation to apply to all  
>>> the
>>> other Nat*.nii files as well.
>>>
>>> The bash scripting bit that does the jobe looks like this
>>>
>>> for PREFIX in PREFIXES; do
>>>
>>>     # all Nat's except NatAverage
>>>     NATS=${PREFIX}Nat[BMNSV]*.nii
>>>
>>>     echo "computing standard space mapping"
>>>     ${FLIRT} \
>>>         -in ${PREFIX}NatAverage.nii -ref ${TEMPL} \
>>>         -out ${PREFIX}StdAverage.nii -omat ${PREFIX}Affine.txt \
>>>         -bins 256 -cost corratio -dof 12 \
>>>         -searchrx -90 90 -searchry -90 90 -searchrz -90 90 \
>>>         -interp sinc -sincwidth 7 -sincwindow hanning
>>>
>>>     echo "applying standard space mapping"
>>>     for NAT in $NATS; do
>>>
>>>         printf "."
>>>         # use FLIRT to apply transformation to other Nat files
>>>         ${FLIRT} -in ${NAT} -ref ${TEMPL} -out ${NAT//Nat/Std} \
>>>         -applyxfm -init ${PREFIX}Affine.txt \
>>>         -interp sinc -sincwidth 7 -sincwindow hanning
>>>
>>>     done
>>>     printf "\n"
>>>
>>> done
>>>
>>> And it works... but it is amazingly slow for the second part (the
>>> -applyxfm bit). It almost seems that flirt starts the  
>>> registration all
>>> over again.
>>>
>>> I assumed that the other *Nat.nii images would just be resampled  
>>> using
>>> the transformation parameters in *Affine.txt. That is correct, is  
>>> it?
>>>
>>> Is there any way to speed up the process? Changing the  
>>> interpolation to
>>> linear seems to have only a marginal effect. Resampling a 90x100x90
>>> volume should be done well inside a second?
>>>
>>> Thanks for any hints
>>> Alle Meije


------------------------------------------------------------------------ 
---
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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