thr0 = accepts probability as low as zero. There is also an image with
thr25 (i.e. voxels with at least 25% probability). In my opinion I
would go at least for thr25 since the thr0 contains many noisy voxels
close to skull/eyes/etc The code I posted lets you choose your desired
threshold (see script
https://code.google.com/p/funpsy/source/browse/trunk/atlases/funpsy_generateHO.m)
in my case I went for thr=30%
E.
On 28 May 2014 21:34, Yang, Daniel <[log in to unmask]> wrote:
> Dear Enrico,
>
> I just tested. The thr0 works really well and can cleanly separate a mask
> into non-overlapping ROIs and those ROIs capture the whole brain!
>
> to be exact, what does thr0 mean?
>
> Thanks again!
> Daniel
> --
> Daniel (Yung-Jui) Yang, Ph.D.
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> Tel: (203) 737-5454
> E-mail: [log in to unmask]
>
> On 5/28/14 1:34 PM, "Enrico Glerean" <[log in to unmask]> wrote:
>
> One option is to use the HO maxprob th0 file that comes with fsl.
>
> Alternatively, you load the probabilistic HO atlas e.g. in matlab, then each
> volume is a Roi. If you take the max over the 4th dimension you see for each
> voxel which roi is more probable. You can see how I did it here
> https://code.google.com/p/funpsy/source/browse/#svn%2Ftrunk%2Fatlases%253Fstate%253Dclosed
> and if you download the file HO_2mm_rois.mat you get a struct with Rois and
> for each Rois the voxel ids.
>
> Best
> Enrico
>
>
> --
> Enrico Glerean (MSc.)
> PhD Candidate, Brain & Mind Laboratory http://becs.aalto.fi/bml/
> BECS, Aalto University School of Science
> 00076 AALTO, FINLAND
> mobile: +358 40 1877599
> email: [log in to unmask]
> www: www.glerean.com
>
>
>
> On 28 May 2014, at 20:12, "Yang, Daniel" <[log in to unmask]> wrote:
>
> Dear all,
>
> Or, alternatively, how to completely divide the brain (cortical area) into
> non-overlapping ROIs per the Harvard-Oxford atlas?
>
> Best,
> Daniel
>
> On 5/28/14 12:56 PM, "Yang, Daniel" <[log in to unmask]> wrote:
>
> Dear all,
>
> I found that the 48 cortical ROIs in the Harvard-Oxford atlas tend to
> partially overlap each other, due to the nature of a probabilistic atlas.
>
> However, it is possible to generate non-overlapping ROIs out of this atlas.
> Is it okay to do threshold/probability >= 50?
>
> Best,
> Daniel
>
|