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The second number is mm3. On Mon, Sep 1, 2014 at 12:08 AM, Gawlitza, Matthias < [log in to unmask]> wrote: > Dear all, > > an additional question on the values that are given in fslstats when using > -V to get a volume of a defined ROI... > > for example I have a segmented ROI on a DWI pic of a stroke patient and > fslstats' ouput is > > "163 2865.234375" > > Okay that means that I have 163 pixels in that ROI, however what is the > unit of the second number (can't be milliliters, that would have to be a > whale or sth. like that...) > > Greets, > > Matthias > > ________________________________________ > Von: FSL - FMRIB's Software Library [[log in to unmask]]" im Auftrag > von "Mark Jenkinson [[log in to unmask]] > Gesendet: Mittwoch, 4. Juni 2014 00:08 > An: [log in to unmask] > Betreff: Re: [FSL] DWI stroke lesion segmentation in a predefined brain > area using a mask > > Hi, > > It is very difficult to know whether this approach using FAST will work > generally on your acquisitions. I would try it and see how it performs. > Since acquisitions vary a lot it is impossible to determine whether such an > approach will generalise well or not, but my experiences are that such > things often need a lot of tuning for different sequences. > > All the best, > Mark > > > On 1 Jun 2014, at 19:03, "Watson, Christopher" < > [log in to unmask]> wrote: > > > You can manually define the ROI using fslview. Since (I think) you're > just going to specify a 3D box, this should be very simple. > > For the FAST stuff, I am unsure, so you will have to wait for one of the > FSL developers to give their suggestions. > > > > Are all of your subjects going to be in the acute stage? As you know, > the signal abnormality on diffusion imaging will change in a matter of days > (perhaps more quickly), so you may get inconsistent results (in terms of, > e.g. delineating the "true" infarct core vs. core + penumbra) if different > subjects have MRI at varying times since stroke. > > > > ________________________________________ > > From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of > Gawlitza, Matthias [[log in to unmask]] > > Sent: Sunday, June 01, 2014 11:11 AM > > To: [log in to unmask] > > Subject: [FSL] DWI stroke lesion segmentation in a predefined brain area > using a mask > > > > Hello everybody, > > > > what I am trying to do is to semiautomatically segment stroke lesions. > Basically I would like to do it like Petkova et al. in 2010 (--> > http://www.ncbi.nlm.nih.gov/pubmed/21045177). > > > > Besides providing an image (see below) they described their way of > segmentation (after BET and registration which is no problem) as follows: > "... (c) manual three-dimensional definition of a mask encompassing the > area of high signal intensity on DW images followed by automatic > three-dimensional stroke segmentation (Functional Magnetic Resonance > Imaging of the Brain automated segmentation tool) (briefly, this > corresponded to segmentation of the DW voxels within the mask into six > gray-level classes, keeping only voxels of the two highest classes)..." > > > > > > [cid:b0542797-8ac5-47e2-bb0d-a6408575d5d5] > > > > > > This seems like a pretty good idea - by defining a mask roughly > encompassing the stroke area and constraining the FAST segmentation to this > region one could exlude all other "bright voxels" in the brain from > inclusion into the segmentation. > > > > > > Maybe anyone has an idea on how to accomplish this? > > > > > > Thanks a lot and best regards, > > > > > > Matias > -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]