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Jason, So far our most reliable lateral ventricle segmentations come from applying itksnap's semi-automated segmentation to FSL's hard-segmented output from FAST. T1 -> (FSL's FAST) => hard-segmented 3-tissue-type map -> (itksnap semi-automated segmentation) => latven mask best, Stephen On Wed, Apr 9, 2008 at 8:46 AM, Jason Steffener <[log in to unmask]> wrote: > On a similar note... > Does anyone have any methods for extraction of the lateral ventricles? > > Thank you > Jason. > > > ----- Original Message ---- > From: Stephen Towler <[log in to unmask]> > To: [log in to unmask] > > > Sent: Tuesday, April 8, 2008 7:34:56 PM > Subject: Re: [SPM] CSF measurement using segmentation > > Dr. Benson, > > You may be interested in the output of FSL's BET, SIENA > (longitudinal), and SIENAX (single time point). > > http://www.fmrib.ox.ac.uk/fsl/bet2/index.html > http://www.fmrib.ox.ac.uk/fsl/siena/index.html > > > best, > Stephen > > > > On Mon, Apr 7, 2008 at 12:07 PM, Benson, Randall <[log in to unmask]> wrote: > > List members, > > > > I am trying to look at age effects on global grey, white and CSF volumes. I can get reliable measurements of GM and WM but CSF is not reliable using segmentation in SPM5. Does anybody know a good way to do it either with SPM or with another program, e.g., FSL? I would greatly appreciate ANY help on this. > > > > Randy > > > > ------------------------------------------------------------------------ > > Randall R. Benson, M.D. > > Assistant Professor of Neurology > > Wayne State University School of Medicine > > UHC-8D 4201 St. Antoine > > Detroit, MI 48201 > > Tel: 313-993-2726 > > Fax: 313-745-4216 > > > > > > > > -----Original Message----- > > From: Benson, Randall > > Sent: Fri 4/4/2008 9:47 AM > > To: John Ashburner; [log in to unmask] > > Subject: RE: [SPM] Segmentation-Results display > > > > So, John and fellow SPMers, > > > > Since we are trying to use SPM5 to do volumetric analysis of WM, GM and CSF, specifically looking at age effects and possibly longitudinal analysis in dementia and TBI patients, we really need either a reliable measure of CSF or at least a good measure of intracranial cavity volume (without dura, skull, etc.). Is there a good way of doing this in SPM proper or extensions of SPM? How have people done these analyses? > > > > Randy > > > > ------------------------------------------------------------------------ > > Randall R. Benson, M.D. > > Assistant Professor of Neurology > > Wayne State University School of Medicine > > UHC-8D 4201 St. Antoine > > Detroit, MI 48201 > > Tel: 313-993-2726 > > Fax: 313-745-4216 > > > > > > > > -----Original Message----- > > From: SPM (Statistical Parametric Mapping) on behalf of John Ashburner > > Sent: Fri 4/4/2008 9:17 AM > > To: [log in to unmask] > > Subject: Re: [SPM] Segmentation-Results display > > > > > We are trying to do volumetric analysis from segmentation using SPM5. We > > > would like to get accurate measurements of GM,WM and CSF volumes. We are > > > running into some problems. > > > > CSF volumes are not likely to be very accurate, as there are no tissue > > probability maps for non-brain tissues. Maybe the skull-stripped version > > would help here - but be careful not to strip out too much CSF. > > > > > > > > 1) We are finding that when we skull strip the MPRAGE, the segmentation > > > algorithm never gives a solution. Has anybody else observed this? > > > > Depending how the skull-stripping is done, it is possible that the orientation > > information in the headers is being lost, or filled with junk. > > > > > 2) When we apply a mask of the brain to the MPRAGE image in segmentation, > > > which of the 3 options (data, probability map, mask) should be used? > > > > Masking is just for cases where there are lesions in the brain, which you > > don't want to influence the way that GM, WM etc in other parts of the brain > > is segmented. > > > > > 3) There is no result displayed on the graphics window after the > > > segmentation program is done- Does anybody know why this is the case? > > > > Because I was too lazy to write the code for displaying the results. It is > > easy to check the results with the Check Reg routine, and this allows you to > > display the images that you consider most useful. > > > > > 4) There is no PS file written in the working directory after the > > > segmentation program is done.- Does anybody know why this is the case? > > > > Again, because I was too lazy. > > > > Best regards, > > -John > > > > > > -- > Stephen Towler > [log in to unmask] > 352-294-0048 office > 352-682-5231 mobile (*NEW*) > 352-392-8347 fax > > Leonard Lab > Department of Neuroscience > PO Box 100244 > University of Florida HSC > Gainesville, FL 32610 > > > >