Dear Bruce and Freesurfer Experts, Thanks for the quick answer, Bruce, to previous post.
As I work my way through all the checks on output I had a couple of other quick questions 1) I noticed by skull-stripping was poor (too aggerssive at the back of the brain with part of the occipital lobe and a small part of cerebellum). I therefore tried a number of suggestions from the tutorials including using -wsthresh 35 and -no-wsgcaatlas - this worked well but could someone explain why the lack of atlas use improves things ? 2) I also tried to improve skull stripping using the talairach_with_skull_2.lta option but I did not have this file despite recon-all -all having run fine the first time around with no errors/problems reported - should this concern me ? 3) I am using Centos 64 on a Linux box with 4 cores and 12 GB of RAM - how many instances of recon-all could I have running at the same time with no problems Thank you. Mo On Thu, Nov 24, 2011 at 4:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Mo, > > that's not a problem. We have different normalizations for different > pieces of the recon. For subcortical we use the norm.mgz, which should > *not* be eroding borders of thalamus, pallidum, etc.... The brain*.mgz are > for cortex, where we don't care about those borders. > > cheers > Bruce > > On Thu, 24 Nov 2011, Mahinda Yogarajah wrote: > > Dear Experts, >> >> I am a beginner to the use of Freesurfer and having just installed version >> 5.1.0 (Centos 64bit) I have been going through the processing pipeline >> with >> one of our own datasets (3T GE Excite II scanner - coronal T1-weighted >> volumetric acquisition sequence with 1.1-mm thick slices). recon-all >> works >> fine and I have been looking at the outputs. >> >> I have a question regarding the subcortical segmentation especially around >> the basal ganglia - during the intensity normalisation it appears to have >> assigned similar high (110) voxel values to parts of the internal capsule, >> pallidum and thalamus (pic1- brainmask.mgz), though the actual >> segmentation >> (pic2-aseg) looks reasonable when compared with the native image (pic3-raw >> T1) (though I appreciate one is normalised and the other is not). Should >> I >> be worried about this (and if so how can I correct ?) or is this intensity >> normalisation used only in the surface stream with a different intensity >> normalisation used in the volume stream ? Or ... is it used in the volume >> stream but the other parts of the model (eg priors from atlas etc) >> compensate in some way. >> >> Thanks. >> >> Mo >> >> PS I can post screen >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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