Hi Doug and Bruce,
When I am running mri_binarize with aseg.mgz as input and --match 77 I get clusters, but when I run the same thing with the orig.mgz as input, I get individual voxels and not any clusters are forming. Could you please explain to me why is this happening and whether there is a way to get clusters with orig.mgz as input?
Thank you for your time. Panos ________________________________________ From: Fotiadis, Panagiotis Sent: Monday, June 10, 2013 4:03 PM To: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] HypoIntense Lesions
Great, thank you!
Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 3:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions
Hi Panos, I don't know an automatic way to do it. You could label it by hand on tkmedit or freeview. doug
On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
Hi Doug,
Thanks for your response, it was really helpful. In addition to the previous comments, I have some subjects that have a hematoma that is not shown in the aseg.mgz file, and hence is not shown as a hypointense cluster after doing the analysis provided below. Do you know if there is any other way to extract information (such as outlining it and/or acquiring its volume) about something like?
Thanks again, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 12:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions
On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
Hi Doug and Bruce,
Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them?
This is already done in recon-all (aseg.mgz and aseg.stats)
In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)?
That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 ------>> This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug
Thanks for your help, Panos ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions
Hi Panos
sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know
cheers Bruce
On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote:
Hi FreeSurfer Community,
I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan.
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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