Dear Michael,
if you use eddy_correct that is fine - there is no need to extra-flirt, since eddy_correct calls
flirt for every volume with the options -nosearch and -paddingsize 1 after extracting the reference
volume (with fslroi).
Have a look at the program itself which is plain text and readable, e.hg. with typing less
${FSLDIR}/eddy_correct.
Best,
Mareike
On 04/27/10 16:10, Subscribe FSL Michael wrote:
> Hello FSL users,
>
> I haven't figured it out myself (non expert in data processing) and would be happy for some assistance. I am analyzing diffusion in the brain. First I eddy correct my data and then I run it through DTIFIT. This is working well, but I would also like to try out FLIRT! I would like to use the b-zero in the diffusion series as a reference image to better align all diffusion directions. Is this possible? If so, how do I extract the b-zero data from the eddy corrected data? Should this be done after DTIFIT?
>
>
> Best regards,
> Michael
>
>
--
Mareike Menz
Institut für Systemische Neurowissenschaften
Universitätsklinikum Hamburg-Eppendorf, Haus W34
Martinistr. 52, D-20246 Hamburg, Germany
+49 40 7410 53683
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