On Wed, 2009-09-02 at 08:37 -0400, Audrey Duarte wrote:
> Hi Christian, I wanted to weigh in with my own results and ask about
> your mask. I followed this procedure you suggest, with a few changes.
> I created binary FOV masks myself for each subject, since I typically
> do first level stats after normalisation. I applied these masks to the
> EPIs after the flow fields had been applied (with smoothing for EPIs
> without for mask). This masking did take care of eliminating voxels
> outside the FOV as does your procedure. However, after applying the
> flow fields (DARTEL deform to MNI) to the mask without smoothing,
> little holes appear in the image which subsequently appear in the EPIs
> after applying the mask. Did you see the same in your mask after
> deforming it to MNI space?
>
> The images from L to R are the EPI deformed to MNI with smoothing, the
> FOV mask for the same subject, the deformed mask without smoothing,
> single subject canonical brain.
> Thanks, Audrey
>
> 2009/9/1 Christian Büchel <
[log in to unmask]>
> Dear Jonathan and Marko,
>
> The problem seems to stem from the combined warping and
> smoothing that is
> performed. It always occurs when your EPIs are truncated.
> Doing some control
> analyses revealed that inside the original EPI everything is
> correct. It's
> just that the deformation field enlarge the voxels outside the
> FOV.
> We have designed a pipeline that takes care of these problems
> (and at the
> same time saves a lot of disk space as only the con images are
> normalized
> and smoothed...).
>
> 1. Coregister T1 onto first functional image
>
> 2. Realign and reslice fMRI, then do first level stats
> (unsmoothed images!)
>
> 3. Use all T1 images --> new segment --> Dartel
>
> 4. Take individual con images from first level analyses and
> apply
> deformations (and smooth) them into MNI space (using
> "normalise to MNI").
> These images will again look funny.
>
> 5. Take the individual mask.img (that was created by the 1st
> level stats)
> and also deform this into MNI (using Dartel) BUT without
> smoothing.
>
> 6. Take all spatially normalised individual mask.img and do a
> logical AND
> (using IMCALC) with all of them and use the ensuing image as a
> mask for the
> final 2nd level stats.
>
>
> I hope this works for you
>
> -Christian
>
> --
> Prof. Dr. Christian Büchel
> Institut für Systemische Neurowissenschaften
> Haus W34, Universitätsklinikum Hamburg-Eppendorf
> Martinistr. 52, D-20246 Hamburg, Germany
> Tel.: +49-40-7410-54726
> Fax.: +49-40-7410-59955
>
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>
http://www.uke.uni-hamburg.de/institute/systemische-neurowissenschaften/
>
> > -----Ursprüngliche Nachricht-----
> > Von: SPM (Statistical Parametric Mapping)
> > [mailto:
[log in to unmask]] Im Auftrag von Jonathan Peelle
> > Gesendet: Dienstag, 1. September 2009 14:57
> > An:
[log in to unmask]
> > Betreff: [SPM] SPM8: DARTEL normalise to MNI problem with
> > partial coverage EPIs
>
> >
> > I've come across a curious normalization issue using the
> > "normalise to MNI" option in SPM8 (with recent updates) on
> > partial-coverage EPI scans. Segmentation, coregistration,
> > and template creation seem to work ok (see
> struct_c1_exampfun.png).
> >
> > Applying the flow field to the segmented structural image
> > seems to be fine. However, when I apply the flow field to
> > the functional data, I get the strange warping attached (see
> > avg152_mwc1_swf.png). This came up at least once previously
> > on the list, but I didn't see any replies:
> >
> >
>
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0908&L=SPM&P=R
> > 399&X=485D484296C56BEE64
> >
> > Have others run into this issue? Any idea what this might
> be
> > due to, and (even better) possible suggestions for ways to
> > fix? Thanks!
> >
> > Jonathan
> >
> > --
> > Jonathan Peelle, PhD
> > MRC Cognition and Brain Sciences Unit
> > 15 Chaucer Road
> > Cambridge CB2 7EF
> > UK
> >
>
>
>
>
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister
> und Genossenschaftsregister sowie das Unternehmensregister
> (EHUG):
>
> Universitätsklinikum Hamburg-Eppendorf
> Körperschaft des öffentlichen Rechts
> Gerichtsstand: Hamburg
>
> Vorstandsmitglieder:
> Prof. Dr. Jörg F. Debatin (Vorsitzender)
> Dr. Alexander Kirstein
> Ricarda Klein
> Prof. Dr. Dr. Uwe Koch-Gromus
>
>
>
> --
> Audrey Duarte, PhD
> Assistant Professor
> School of Psychology
> Georgia Institute of Technology
> 654 Cherry Street
> Atlanta, GA 30332
> voice 404-894-2349
>
http://psychology.gatech.edu/duartelab/
