---------- Forwarded message ----------
From:
mohan boddu <bmohan.boddu@gmail.com>
Date: Tue, Aug 9, 2011 at 6:17 AM
Subject: Re: [Freesurfer] Segmentation of hippocampal subfilelds
To: Koen Van Leemput <
koen@nmr.mgh.harvard.edu>
Hello,
I would like to thank you for the information, but the problem is, I am a CS student working on this and I dont have much idea about it. Basically my task is to convert those images into ROI mask. For this I have to follow the instructions in the website stated below:
http://brainybehavior.com/neuroimaging/2010/06/saving-individual-labels-from-freesurfers-aseg/
But the process stated in the above website works for label maps, and if the images generated in the "
segmentation of hippocampal subfields" (
http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation) (8 images are generated for each side) stage are probability maps then what should be given as upper threshold(-uthr) and lower threshold(-thr) values. And as the last step says to divide it by its label number to normalize it. Is it necessary for the probability maps, if it is, then what would be the number that we have to divide?
Sorry, if I am not clear and thank you very much for helping me out.
On Tue, Aug 9, 2011 at 10:41 AM, Koen Van Leemput
<koen@nmr.mgh.harvard.edu> wrote:
Hi Mohan,
The segmentation results are given as probability maps: a (unsigned
8-bit) value of 0 means probability 0 , 255 means probability 1, and
everything in between scales linearly.
The proper way to obtain "crisp" label maps from these images is to
assign each voxel to the label map that has the highest probability,
so you'd need to read in all probabilty maps, visit each voxel and
compare the probabilities in the voxel for all structures.
Generating such "scrisp", winner-takes-all label maps is not
recommended to calculate e.g., volumes etc, though...
Hope this helps,
Koen
On Mon, Aug 8, 2011 at 2:26 PM, mohan boddu <
bmohan.boddu@gmail.com> wrote:
> I have completed the segmentation of hippocampal subfileds, but now I would
> like to know the generated images are in probability map or label map? If
> they are in label map what would be the best upper and lower thresholds to
> generate the ROI mask images. Could you please also tell me the way to do
> so.
>
> --
> --Mohan Boddu--
> Research Assistant
> Department of Radiology and Imaging
> Research II Building
> Indiana University School Of Medicine
> Indiana University-Purdue University Indianapolis
> Indianapolis, IN 46202
>
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--
--Mohan Boddu--
Research Assistant
Department of Radiology and Imaging
Research II Building
Indiana University School Of Medicine
Indiana University-Purdue University Indianapolis
Indianapolis, IN 46202