Hi, yes it is worth getting the first stage of the FIRST scripts (the
standard space registration) working accyurately, though note that
this uses a subcortical mask to optimize registration in the
subcortical area, so may not look globally otimal. Cheers
--------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]
http://www.fmrib.ox.ac.uk/~steve
----------------------
On 20 Feb 2009, at 18:15, Liam Nestor <[log in to unmask]> wrote:
> Hello there FSL people.
>
> I am new to FSL First. I am currently using first_flirt and
> run_first to
> perform alignment and segmentation of subcortical structures, which
> I then
> compute the volume of (nonzero voxels) using fls_stats.
>
> I have scripted this whole process and everything seems to be
> working very
> well. I have noticed, however, some of my T1-weighted images in
> native space
> are not particularly straight (i.e. a bit twisted - not well
> aligned). I
> understand that we transfer our image in native space to 152MNI, but
> segmentation actually takes place on the image in native space.
>
> My main question is whether images not well aligned in native space
> are
> likely to have an effect on the integrity of the segmentation
> process? If it
> is, does FSL have a programme to straighten up the images in native
> space.
>
> Many Thanks,
>
> Liam.
>
>
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