Hi Colin,
> I used the unwarp procedure with fieldmaps to motion correct my data. I
> later discovered that the slice order in my previous step (slice time
> correction) was incorrect. I had to go back and redo the slice time
> correction. Now I'm wondering if I have to re-run the unwarp
> estimate/reslice procedure (a 12 hour proposition), or if I can just
> reslice the data using realign:reslice.
>
> 1. Will changes to the slice time correction result in changes to the
> unwarp estimation (should I redo it)?
I would redo it. I maybe wrong but I would strongly suspect that (since
doing slice timing differently changes your voxel intensities) this may
interfere with any following processing step.
> 2. If not (1), will realign:reslice apply the transformations from the
> previous unwarp estimate to my new resliced data?
I do not think so: the "simple" realingment is a rigid body procedure,
which is usually encoded in the header (hence you rarely need to write
out realigned images). Unwarping is non-linear as it accounts for the
EPI distortions and the non-linear interactions of the head with the
magnetic field; these changes cannot be encoded in the header and thus
require the images to be written out. You can apply the unwarp
information (if you saved it) to any given dataset if you play with the
fieldmap code but given that you change the input files that should
enter the unwarping procedure, I would redo the whole thing.
Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn/
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