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SPM  October 2013

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Subject:

Re: Normalization and Orientation Issue

From:

"Harms, Michael" <[log in to unmask]>

Reply-To:

Harms, Michael

Date:

Fri, 18 Oct 2013 19:00:47 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (75 lines)

Hi,
Just thought it worth mentioning that the order of motion correction vs.
slice timing correction (if used) is one of the differences between SPM
and FSL.
For a more detailed post regarding the FSL rationale for doing motion
correction first, see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1208&L=FSL&D=0&1=FSL&9=A&
J=on&d=No+Match%3BMatch%3BMatches&z=4&P=29105

cheers,

--
Michael Harms, Ph.D.

-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.           Tel: 314-747-6173
St. Louis, MO  63110                    Email: [log in to unmask]




On 10/18/13 1:03 PM, "H. Nebl" <[log in to unmask]> wrote:

>Dear Balu,
>
>
>when conducting single-subject analyses the data has to be resliced at
>some point (this is done during normalisation step otherwise). As Marko
>stated, during "Realignment: Estimate" the headers of the images are
>adjusted, but the data itself is not resliced (motion parameters are not
>applied to the data). This means one voxel in volume 1 does not
>correspond to the same voxel in volume 2. However, during slice timing
>motion parameters are NOT applied to the data either (nor during
>smoothing). To solve this issue you have to reslice your data somewhere.
>Otherwise you get some error similar to yours when trying to run
>single-subject models. The same error might occur during group statistics
>if data from different subjects weren't normalised the same way
>(something like different bounding box) or if you try to run group
>statistics on data in native space.
>
>Concerning the order of slice timing and realignment see
>http://mindhive.mit.edu/node/109 for more information. With interleaved
>acquisiton scheme it is probably better to start with slice timing [if
>you expect rather large motion between subsequent scans then slice timing
>introduces some error indeed, but in this case your data is rather
>problematic anyway. Then your data suffers from motion artefacts and you
>should probably avoid slice timing completely or at least, replace
>affected volumes - otherwise you transfer artefacts from an affected
>volume to neighbouring unaffected volumes]. So for analyses in native
>space go with ST -> "Realignment: Estimate & Write", when using
>normalisation go with ST -> "Realignment: Estimate".
>
>If you don't want to start with slice timing, then you HAVE to use
>"Realignment: Estimate & Write" as far as I can see, even if your
>preprocessing pipeline includes a normalisation step. Otherwise you
>correct temporally within your original slices, which is exactly not what
>you want when starting with realignment. You can try yourself if you
>"realign manually" via the Display function and flip one volume along y
>for example (resize(y) = -1). After slice timing the temporally
>neighbouring volumes should have different values then, depending on
>whether you use the original data or the time series with the flipped
>volume. But they do not.
>
>
>Best,
>
>Helmut


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