I use FLIRT to align diffusion data. I used the first volume, so no
diffusion. I did extract the brain with fractional intensity threshold
set to 0.3 because the default 0.5 was removing too much. And I used
avg152T1_brain.hdr as reference image.
Anna
Quoting Stephen Smith <[log in to unmask]>:
> What data are you feeding into FLIRT? I assume that this is diffusion
> data, are you using the nodif
> image for the flirting? Did you brain extract the input data? Did you
> use the brain-extracted MNI
> template or the whole-head?
>
> Steve.
>
>
> On Thu, 18 Jan 2007 12:36:14 +0100, Anna Rotarska-Jagiela <[log in to unmask]
> FRANKFURT.DE> wrote:
>
>> Dear FSL experts, I aligned three datasets using FLIRT to MNI template
>> provided by FSL and re-sampled to 1x1x1mm in MRIcro. The alignment for
>> the first dataset worked very well, it failed completely for the second
>> one, and is somewhere half-way for the third. Why? It’s the same
>> sequence, the same pre-processing (eddy current correction) only
>> different participants. Do you have any explanation for this? Any tips?
>> Thank you in advance for your help. Greetings,
>>
>> Anna Rotarska-Jagiela
>>
>> --
>> Anna Rotarska-Jagiela, M.S.
>> Universitätsklinikum Frankfurt
>> Zentrum der Psychiatrie Labor für Neurophysiologie and Neuroimaging
>> Heinrich-Hoffmann-Str. 10
>> 60528 Frankfurt am Main
>> Germany
>>
>> Tel.: +49(0)69 6301 5389
>> Fax.: +49(0)69 6301 3833
>> Email: [log in to unmask]
>> Web: http://www.bic.uni-frankfurt.de/
>> ===========================================================
> =============
>
--
Anna Rotarska-Jagiela, M.S.
Universitätsklinikum Frankfurt
Zentrum der Psychiatrie Labor für Neurophysiologie and Neuroimaging
Heinrich-Hoffmann-Str. 10
60528 Frankfurt am Main
Germany
Tel.: +49(0)69 6301 5389
Fax.: +49(0)69 6301 3833
Email: [log in to unmask]
Web: http://www.bic.uni-frankfurt.de/
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