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Hm - wasn't the reason to set the probability everywhere to non-zero one or two SPM versions ago exactly that - if there really was GM in unusual places (as happens regularly with epilepsy patients' heterotopia, *particularly* around the ventricles), then the clear message from the histogram could "override" the very low but non-zero probability from the a priori maps? I for one would be very unhappy with a zero prior probability map in these areas... and for subjects with non-malformed brains, I've always found that the *tiny* rim of misclassified voxels around the ventricles is a rather endearing feature that maps the outline nicely. Excuse my ignorance, but in which application is this really a problem? Please be aware that there may be downstream implications when such changes are made! Many thanks as usual, Alexander -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On Behalf Of Ashburner John (PSYCHOLOGY) Sent: 11 January 2007 19:48 To: [log in to unmask] Subject: Re: [SPM] Segmentation difficulties in the deep GM The best chance would be via a modified set of tissue probability maps. If these indicated that the prior probability of finding grey matter in these regions was zero, then the posterior probabilities of finding GM here would also be zero. Generating such corrected maps sounds like a potential job for the ICBM consortium. All the best, -John -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Simon B. Eickhoff Sent: Thursday, January 11, 2007 7:25 PM To: [log in to unmask] Subject: Re: [SPM] Segmentation difficulties in the deep GM Hi John! A sort-of follow-up on that topic. When segmenting any sort of image, I almost always get a "rim" of grey matter voxels surrounding the ventricles. Some of this is the caudate of cause, but most other stuff looks like misclassified partial volume effects between ventricle and white matter. Is there any way to get around these, any suggestion how to fix that (within SPM) Thanks in advance Simon ----- Original Message ----- From: "Ashburner John (PSYCHOLOGY)" <[log in to unmask]> Date: Thursday, January 11, 2007 7:14 pm Subject: Re: [SPM] Segmentation difficulties in the deep GM > This is (kind of) mentioned in my Unified Segmentation paper of > last year, which describes the segmentation method in SPM5: > > The simple model of grey matter being all of approximately > the same intensity could also be refined by using tissue > probability maps for various internal grey matter structures > (Fischl et al., 2002). > > > There are loads of papers out there that describe ways of trying > to segment these internal GM structures, and the associated > problems, but you may need to look in journals such as IEEE Trans. > Med. Imag., or various medical imaging conference proceedings. > > Best regards, > -John > > -----Original Message----- > From: SPM (Statistical Parametric Mapping) > [mailto:[log in to unmask]] On Behalf Of Bastos Leite, Antonio > Sent: Thursday, January 11, 2007 5:40 PM > To: [log in to unmask] > Subject: [SPM] Segmentation difficulties in the deep GM > > Dear Marko and list, > > According to the information posted below, I recently noticed the > existence of segmentation difficulties in the deep GM, > particularly in the putamen and thalamus, due to the lack of > sufficient contrast with the surrounding WM of T1-weighted images > (T1-WI). > > Since this seems to be a known problem and probably there is not a > solution for it, at least I would like to be informed if there are > bibliographic references reporting it. So far, I couldn't find them... > > Regards, > > Antonio > > -----Mensagem original----- > De: SPM (Statistical Parametric Mapping) > [mailto:[log in to unmask]] Em nome de Marko Wilke > Enviada: segunda-feira, 18 de Dezembro de 2006 7:39 > Para: [log in to unmask] > Assunto: Re: [SPM] increased pons intensity in white matter VBM > > Hi there, > > > Recently, I finished VBM analysis in my mTLE study. > > Congratulations :) > > > And I found increased white matter intensity in pons area. > > Because pons is classified into white matter in SPM segmentation, > > I thought this finding came from the neuronal loss (seizure > damage) of pons. > > You may want to be very careful in interpreting such findings as > the > pons, as you say, is segmented into gray and white but it is among > the > structures in the brain that are difficult to segment (as is the > thalamus). So it may be a case of segmentation leaning this way in > a > patient and that way in a control. I do not know about your group > sizes > but I have seen one badly segmented brain screwing up an analysis > of > > 100 brains (which I fortunately noticed before submitting :) > > > Does it make sense? > > Not to me but I am not an epileptologist. There certainly are > indications of pontine networks implicated in seizures but I would > be > extremely careful before drawing such conclusions from a VBM study. > Best, > Marko > > -- > ===================================================================== > Marko Wilke (Dr.med./M.D.) > [log in to unmask] > > Universitäts-Kinderklinik University Children's Hospital > Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology) > Hoppe-Seyler-Str. 1, D - 72076 Tübingen > Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473 > ===================================================================== > > ----------------------------------------- Simon Eickhoff Institut for Medicine (IME); Research Center Jülich Leo-Brandt-Str. 5; 52425 Juelich, Germany Phone + 49 2461-61-5219 / Fax + 49 2461-61-2820 e-mail: [log in to unmask] / [log in to unmask]