Hi - yes, we don't generally recommend using slice timing correction
in FEAT, and so yes I would not worry about these orientation changes,
as long as you are sure that you're not getting left and right mixed up.
Cheers.
On 5 Jun 2008, at 21:03, Diederick Stoffers wrote:
> Dear all,
>
> We have been using a combination of fslswapdim, fslorient -setqform
> and fslorient -copyqform2sform to get both our structurals and
> functionals, which are in NIfTI format, into the standard fslview
> orientation so that we can do fMRI analysis.
>
> Unfortunately we need to reorient our functionals and structurals
> because of the way they come off the scanner and the way they are
> preprocessed into NifTI. There is a preprocessing step that turns
> them into NifTI before we can use a tool such as dcm2nii.
>
> Although our reorientation method using FSL tools appears to work
> well, we are now concerned about the reorientation of the
> functionals, i.e. several websites mention that it is not a good
> idea to reorient 4D data because of issues with slice timing. As we
> don't typically use slice timing correction in FSL-FEAT (even for
> our event-related designs - BTW: should we really be using it
> maybe?), we thought our reorientation would not cause any problems
> in our analyses. Can anybody confirm that this is a valid way to go
> about things?
>
> Thanks
>
> Diederick
>
>
>
> Diederick Stoffers, MS
> Clinical Researcher
> Department of Psychology
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093-0109
> United States of America
> Phone: +1 858 822 2129
> Fax: +1 858 534 7190
> Skype: dstoffers
> Web: www.aronlab.org
> P Please consider the environment before printing this e-mail
>
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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)
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