Hi Patrick,
let me have a stab at that...
> *** Slice Timing - Acquisition was interleaved. It appears in the
> manual that slice timing correction is being discouraged now... why is
> that? Is this true even of interleaved sequences, and if so how is
> the temporal gap between adjacent slices resolved?
The idea behind using it, as you say, is closing the temporal gap
between the acquisition of different slices. The idea behind not using
it is that in most instances, this will not matter (block design),
and/or that the disadvantages (more interpolation, difficulties
recovering the correct timeseries due to motion etc.) will outweigh the
advantages.
> Realign: Estimate and Reslice - Reslice mean image only
>
> Coregister: Estimate - Reference image is mean resliced image; source
> image is subject's structural image
Sounds reasonable, with one exception: if your head position is a bit
off it may be a problem for new segmentation as the initial affine
registration has been changed and seems less stable to me in some cases.
Therefore, it is recommended to do a coregistration (!) of the
anatomical to a T1 template (this will not enlarge/normalize the
anatomical but it will improve the starting estimate for the initial
affine registration). In this case, I would rather coregister T1 to
template and then coregister mean EPI to T1, as changing the orientation
of the T1 after new segment is not advisable (nigh impossible to change
the orientation in the seg8-file...)
> **** Normalise: Write - Images to write are the realigned images. For
> the parameter file, do I include both the segmentation parameters and
> the realignment parameters, or just the segmentation parameters?
Just the segmentation parameters (it should not allow you to include
both anyway). The orientation changes of realign: estimate are encoded
in the headers - check their modification time.
> Smooth - Smooth the normalised files
Sounds reasonable ;)
Best,
Marko
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
=====================================================================
