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As an alternative, if you are interested primarily in the segementation/normalization I found that first coregistering the image you want to segment to the grey matter TPM and then running the segmentation works excellent. In fact, we encountred problems like your in about 5% of the cases without this initial step but never after realignment. If you are interested in modulated VBM, however, you need to account expansion/shrinkage by this initial realignment as well. best Simon ________________________________________ Von: SPM (Statistical Parametric Mapping) [[log in to unmask]]" im Auftrag von "John Ashburner [[log in to unmask]] Gesendet: Montag, 14. Mai 2012 14:55 An: [log in to unmask] Betreff: Re: [SPM] Structural MRI Segmentation All the problems here are due to poor initial affine registration. I would suggest double checking your initial alignment to the tissue probability maps via Check Reg. The initial affine alignment in New Segment is much more stable than that obtained via the Segment button, so I would generally expect to see fewer such problems. Best regards, -John On 14 May 2012 13:37, Nieuwenhuis-4, M. <[log in to unmask]> wrote: > Dear SPM experts, > > In the process of segmenting structural MRI scans I have encountered several strange problems. > I have added a screenshot of some of the (gray matter) segmentations. As you can see, some > scans appear to be almost empty, or have strange artificial stripes, or even have parts missing of > the brain. > > Even though I understood that orientation and origin don't have to be exact, I experience that by > slightly changing the orientation or origin can results in very different kind of segmentations. > > Sometimes one bad segmented scan will be perfectly fine after adjusting the origin only slightly > (+1 voxel up or to the right or 0.01 pitch, yaw or roll) > > The scan's that were not segmented correctly don't have any visual anomalies that could explain > the flawed segmentation. (I have added a screenshot of those scans, same order as the segm.) > > Which brings me to the following questions: > > - Are the segmentations that were bad before, but after adjustment looked visually fine, trustworthy? > - Is there a way (without endlessly trying to adjust the origin and re segmenting) to "fix" the > segmentation of other scans. > > The segmentation is done in SPM8 with the "segment" in the main menu, after applying non uniformity correction (Sled et al.) > > Kindest regards, > > Mireille Nieuwenhuis | Neuroimaging Research Group | Department of Psychiatry | University Medical Center Utrecht | Heidelberglaan 100, 3584 CX Utrecht, the Netherlands | E-mail: [log in to unmask] | Currently at UCL and IoP in London (till the end of july 2012) > > ------------------------------------------------------------------------------ > > De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is > uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht > ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct > te informeren door het bericht te retourneren. Het Universitair Medisch > Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. > (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij > de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. > > Denk s.v.p aan het milieu voor u deze e-mail afdrukt. > > ------------------------------------------------------------------------------ > > This message may contain confidential information and is intended exclusively > for the addressee. If you receive this message unintentionally, please do not > use the contents but notify the sender immediately by return e-mail. University > Medical Center Utrecht is a legal person by public law and is registered at > the Chamber of Commerce for Midden-Nederland under no. 30244197. > > Please consider the environment before printing this e-mail. ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unseren neuen Film? http://www.fz-juelich.de/film Kennen Sie schon unsere app? http://www.fz-juelich.de/app