Hello,
I'm trying to create a canine atlas to use in freesurfers recon-all pipeline. I
want to be able to perform cortical thickness measurements. I have manually
skull-stripped 10 beagle brains. I have used fsl's FLIRT and FNIRT to make an
averaged image of these 10 brain images in nifti forma
Dear FreeSurfer Developers,
Currently we are trying to analyze our functional data (optical imaging)
using ROI’s that are defined on the basis of FreeSurfer Segmentation. In
order to do this, we need a 3 dimensional mask in which a particular region
as identified by FreeSurfer is used as a mask
I am 100% sure that the stimuli themselves are correct (clockwise and
counterclockwise/ expanding and contracting).
When I look at the individual angle values I noticed that the difference
between the cw and ccw is on average equal to half a cycle (so pi).
When I plot the results (using the re
Hi Jordan
sorry, this one slipped through the cracks. There really is no way except
visual inspection, and thalamus is particularly hard. You need to play
with the brightness/contrast to really see the lateral borders, and even
then it can be difficult depending on your acquisition.
cheers
B
When using the norm.mgz, what is the best way to evaluate the accuracy of the
thalamus labeling? If lateral thalamus has low contrast with WM, how can we
tell where its borders should be? Or is it best to assume that the automatic
segmentation has done sufficiently well?
Jordan Pierce
The Uni
Hi Doug,
Thank you, that worked perfectly.
Best wishes,
Clare
Date: Tue, 31 Jul 2012 14:30:50 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] Recon-all -qcache curvature error &
recon-all make -all
To: freesurfer@nmr.mgh.harvard.edu
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