Mark,
Thanks for the clarification. My multi-slice (hence 3D) data is cardiac
gated for every single slice, hence 2D registration for each slice is
what I wanted.
By "appropriately pad in the through-slice direction", do you mean it
registers the first slice between the -in and -ref 3D volume and then
applies the transformation matrix in the through-slice for the rest of
the slices?
If that's case, what I was doing was not desired because the cardiac
gating nature renders distinct motion for individual slices. Yet I'm not
concerned about the alignment between the slices at all (I know this is
weird for the brain paradigm). As long as each slice is aligned
through-volume, through-slice alignment means little to my application.
Seems I have to extract slices from the 3D volumes, register them with
the -2D flag, then assemble them back into 3D volumes. Does that sound
right?
Regards
Gordon
On 11/27/2009 03:04 AM, Mark Jenkinson wrote:
> Hi,
>
> All the sch2D_* files control the number of degrees of freedom
> used for the registration. The -2D flag specifies that it should
> use the sch2D_3dof degrees of freedom *and* to expect a
> single slice, and appropriately pad in the through-slice direction
> (for internal code reasons).
>
> The last dof in the 6dof case is a x-y shear (or skew).
>
> You can run any of the 2D schedule files with 3D data. It simply
> applies the 2D transformation to all slices. You can use any of
> the schedule files with 3D data, without using the -2D option.
> It should work fine. I'm not quite sure what exactly you are
> saying went wrong, but try it without the -2D option (but still
> with the -schedule) and see if that works OK. Make sure you
> have a 3D volume for both input and reference though, as
> otherwise it won't work correctly.
>
> All the best,
> Mark
>
>
> On 27 Nov 2009, at 06:29, Junqian Gordon Xu wrote:
>
>> I want to make sure my understanding of the flirt 2D registration
>> correct.
>>
>> ${FSLDIR}/etc/flirtsch
>>
>> 1) sch2D_3dof (same as -2D): x, y translation + in-plane roation
>>
>> 2) sch2D_5dof: sch2D_3dof + x, y scaling?
>>
>> 3) sch2D_6dof: sch2D_5dof + ?
>>
>> 4) Although the example on line suggests flirt -2D for a single slice,
>> it apparently worked with 3D volume images as well in my trial. The
>> obvious problem is that it only outputs ONE, instead of slice#,
>> transformation matrix, which made me worried about whether I am
>> abusing flirt -2D. However the resulting image did show improvement in
>> alignment and did suggest the code operated on individual slice. Yet,
>> can somebody know the details about flirt -2D verify its behavior in
>> such situation?
>>
>> Thanks
>> Junqian "Gordon" Xu
>> National Multiple Sclerosis Society Postdoctoral Fellow
>> Department of Neurology
>> Washington University in St. Louis
>>
>
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