Yep, we were using full search. I'm not sure where the registration
report page is, sorry.
The files should be available at the following:
Volume: http://www.brainmapping.org/fsl/3dvolEQ_brain_007.img (and .hdr)
16-slice EPI: http://www.brainmapping.org/fsl/whole_func.img (and .hdr)
Sample 3-slice volume from timeseries:
http://www.brainmapping.org/fsl/example_func.img (and .hdr)
Thanks much for your help. Please feel free to email me directly at
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On Saturday, July 26, 2003, at 03:48 AM, Stephen Smith wrote:
> Hi - hard to say - looks like you are probably trying the right things
> -
> if you can make the data available on a website we'll take a look. When
> you look at the registration report page, which of the various steps is
> the problematic one? For the 16-slices EPI to anatomical flirting, did
> you
> turn on full search?
>
> Thanks, Steve.
>
>
>
> On Fri, 25 Jul 2003, Richard Albistegui-DuBois wrote:
>
>> I am trying to use FLIRT to align a very limited set of slices with a
>> 3d T1 volume. I have tried it following the instructions for limited-z
>> datasetson the website, as well as with more standard techniques, and
>> they both give me the same incorrect results.
>> What I have:
>> A functional timeseries of three oblique (mostly coronal, rotated
>> slightly toward axial) 3mm/0 skip slices
>> An anatomical EPI set of 16 slices, including the three in the above
>> set
>> A T1 3d volume taken on a different day
>>
>> When I do FLIRT with timeseries--(3 DOF)-->anatomical--(12
>> DOF)-->volume, the end result has the correct rotation, but is not in
>> the correct place. Aligning the anatomical alone to the volume with 12
>> DOF is similar--it is rotated correctly, but placed incorrectly. It's
>> about 1-2 cm too anterior.
>>
>> I've also tried this with the ventricles weighted, with no change in
>> results.
>>
>> Can anyone offer a suggestion?
>>
>> Richard Albistegui-DuBois
>> UCLA Brain Mapping
>> 660 Charles Young Drive South, Room 237
>> (310) 206-4456 phone
>> (310) 794-7406 fax
>> [log in to unmask]
>> AIM: dubistegui
>>
>
> Stephen M. Smith MA DPhil CEng MIEE
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
>
Richard Albistegui-DuBois
UCLA Brain Mapping
660 Charles Young Drive South, Room 237
(310) 206-4456 phone
(310) 794-7406 fax
[log in to unmask]
AIM: dubistegui
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