Reply-To: | | [log in to unmask][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 > > [log in to unmask] > > > 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=485D484296C5ãLW—6 |