Dear Julie,
I applied the VBM8 skull-stripping approach across a wide range of different data like ADNI, IXI, and the NIH child development data without any problems. In fact I use the segmentations of the New Segment toolbox for the initial skull-stripping in VBM8 with some additions to remove non-brain parts more aggressively. Furthermore, skull-stripping also uses the old (modified) clean-up procedure and finally another masking approach based on morphological operations. This 3-stage approach leads to reliable results (for some results see: http://sve.loni.ucla.edu/archive). Anyway, there might be still difficulties with some data, but the deviating results of Franz are caused by comparing images in different spaces (DARTEL vs. default normalization).
Regards,
Christian
____________________________________________________________________________
Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752 Fax: ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de
On Wed, 17 Nov 2010 08:09:21 -0500, Julie E McEntee <[log in to unmask]> wrote:
>Dear Franz, Christian-
>
>Depending on image sequence/quality, if you are having problems removing dura/skull adequaltely using/tweaking SPM/VBM8 toolboxes inhomogeneity correction/regularization parameters, you can try using another program (e.g., FSL- BET, MIPAV- N3 & SPECTRE) that may do a better job.
>
>Christian, if one were to do this, would any changes need to be made to VBM8 toolbox processing if beginning with skull-stripped images?
>
>Any comments from anyone else on what considerations, if any, when using SPM's New Segment for VBM if beginning with skull-stripped images?
>
>HTH-
>
>-Julie
>
>Julie E. McEntee, MA, CCRP
>Image Processing Technologist
>Center for Neuroscience & Regenerative Medicine, NIH/USUHS
>The Henry M. Jackson Foundation for the Advancement of Military Medicine
>NIH Clinical Center
>B1N264B
>301-451-1869
>[log in to unmask]
>
>Department of Psychiatry & Behavioral Sciences
>Division of Psychiatric Neuroimaging
>The Johns Hopkins School of Medicine
>[log in to unmask]
>
>On Tue, 16 Nov 2010 14:44:25 +0100, Franz Riederer <[log in to unmask]> wrote:
>
>>Dear all,
>>
>>I see there is a lot of effort to support people working with structural MRI
>>analyses, and I am grateful for that. Although I got some inspiration from
>>the archives of the mailing list, I could not find an answer for the
>>following problem:
>>In some rare instances grey matter seems classified as white matter (please
>>see attachment, blue arrow). In these instances, the dura over the cortex
>>appears rather bright (lower image). Changing the bias regularisation to
>>"extremely light" instead of the default "very light" seemed to have a minor
>>positive effect.
>>
>>To my surprise, the Unified Segmentation within SPM8 seemed to be less
>>sensitive to this artifact.
>>
>>I also see that this might be a problem of the sequence we used in this
>>subject.
>>
>>I wonder whether there is a way to optimize post processing.
>>
>>Many thanks in advance,
>>
>>
>>Franz
>>
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