As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects that we had to exclude for what sounds like a very similar reason -- we just couldn't get the pial surface in the anterior temporal lobe to properly encapsulate the gray matter.
-Mike H. On Fri, 2009-05-15 at 12:24 +1000, Olivier Piguet wrote: > That is correct. This is case of semantic dementia where left anterior > temporal region is markedly atrophic. > Olivier > > On 15/05/2009, at 9:15, Bruce Fischl wrote: > > > so there's 10mm or so of gray matter with no underlying wm? I didn't > > think that was ever the case. What pathology is this in? And you're > > sure it's cortex, not amygdala? Jean: any thoughts? > > > > On Fri, 15 May 2009, Olivier Piguet wrote: > > > >> Hi Bruce, > >> In the coronal plane, slice 152 is the last slice where white > >> matter is clearly visible. Then, slices 153-158, only grey matter > >> is recognised but not all of it, and slices 159-164, grey matter > >> is not recognised at all. > >> I added control points on slice 151-153 in the hope that it would > >> help but no luck. > >> Olivier > >> > >> On 15/05/2009, at 8:39, Bruce Fischl wrote: > >> > >>> Hi Oliver, > >>> how far away is the nearest white matter? > >>> Bruce > >>> On Fri, 15 May 2009, Olivier Piguet wrote: > >>>> Hi there, > >>>> I haven't received a reply to my question below. > >>>> Just to clarify, I ran autorecon1 and autorecon2 on this subject. > >>>> When examining the surfaces in tkmedit, the left temporal pole is > >>>> not included in the pial surface. Is there a way to force > >>>> freesurfer to recognise this as valid brain tissue, bearing in > >>>> mind that there is no visible white matter underneath (and > >>>> therefore the option of adding control points is not possible). > >>>> Thanks for any suggestion to resolve this problem. > >>>> Olivier > >>>> On 13/05/2009, at 12:57, Olivier Piguet wrote: > >>>>> Hi there, > >>>>> I've run autorecon2 on a subject who has significant unilateral > >>>>> atrophy in the anterior temporal region. In the last few slices > >>>>> anteriorly, the pial surface does not include what is clearly > >>>>> atrophied cortical tissue without underlying white matter. What > >>>>> is the method to correct for this? Looking at previous queries, > >>>>> all of them refer to spots where one can manipulate the > >>>>> segmentation by adding control points in the neighbouring white > >>>>> matter, which is not present in this instance. > >>>>> Any suggestion appreciated. > >>>>> Olivier > >>>>> ~~~~~~~~~~~~~~~~~~~~~ > >>>>> Olivier Piguet Ph.D. > >>>>> NHMRC Fellow (Clinical Career Development Award) > >>>>> Conjoint Senior Lecturer UNSW > >>>>> Prince of Wales Medical Research Institute > >>>>> Barker St > >>>>> Randwick NSW 2031 > >>>>> Australia > >>>>> Voice: +61 2 9399 1113 > >>>>> Fax: +61 2 9399 1047 > >>>>> E-mail: o.pig...@powmri.edu.au > >>>>> <pastedGraphic.tiff> > >>>>> http://www.ftdrg.org/ > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
