[Freesurfer] weird tksurfer display

i setup freesurfer out of MGH, and run the following command as you recommend to test the installation. tksurfer bert rh pial and i got this; surfer: current subjects dir: /disk3/ans2/ansfreesurfer/subject/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir

Re: [Freesurfer] weird tksurfer display

don't know what means 'surfer: ### redraw failed: no gl window open' in the terminal message... the only error message i got is this. On Fri, Sep 4, 2009 at 5:54 PM, jeungchan lee wrote: > i setup freesurfer out of MGH, and run the following command as you > recommend to test the installation. >

Re: [Freesurfer] Fwd: selecting the best structural scan

Along the same vein, I found this page on the freesurfer site: http://surfer.nmr.mgh.harvard.edu/fswiki/QATools but it doesn't seem to link to any actual tools? have these been discontinued? -Alex ~)- -- Alexande

Re: [Freesurfer] Fwd: selecting the best structural scan

Hi Sima, I've run 6 versions of the same scan of the same subject I got some differences too. Not so big as you found but still some differences Probably it's the -randomness flag in the recon-all Check: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html

[Freesurfer] selecting the best structural scan

Hi Pedro, Thanks for your reply, Actually I am using 6 different sequences for scanning the same subject, so a small part of the difference could be because of randomness, but there should be a way to select the best scan from these 6 different scans. I need to know how to select the best. any su

Re: [Freesurfer] Fwd: selecting the best structural scan

I have an experiment with 3 different sequences, but the maximum difference I've found was 5% --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilt

Re: [Freesurfer] selecting the best structural scan

Hi Sima, you could compute the contrast-to-noise ratio between gray and white, which will give you some idea. The overall optimization is very difficult though as there are factors like distortion, contrast uniformity, etc cheers Bruce On Fri, 4 Sep 2009, sima chalavi wrote: Hi Pedro,

Re: [Freesurfer] Wrong boundaries at ventricle.

HI Bruce, Zheng Hui and all. I just wanted to add that we have also seen the same issues in our data that was been updated from 3.5. However, I noticed this issue started to occur around version 4.20 with another data set of ours. Many of us had assumed that this was the new way Freesurfer segme

Re: [Freesurfer] weird tksurfer display

Jeungchan, Try updating the nvidia driver (assuming your system has an nvidia card). That is: sudo /sbin/init 3 sudo nvidia-installer --update 'sudo' is not necessary if you can su to root. If this is an NMR center machine, email help and they can do this for you. Nick On Fri, 2009-09-04 at

Re: [Freesurfer] Wrong boundaries at ventricle.

Zheng, Can you send me the following files to our file drop? wm.mgz, wm.seg.mgz, brain.mgz and aseg.mgz The file drop is https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Also, were edits made to wm.mgz? I see from the log that it is being treated as if there were (although I need

Re: [Freesurfer] Wrong boundaries at ventricle.

thanks Judith, this is a bug that should be pretty easy to fix if someone can send us a sample set that it occurs on. cheers, Bruce On Fri, 4 Sep 2009, Judith Segall wrote: > HI Bruce, Zheng Hui and all. > > I just wanted to add that we have also seen the same issues in our data > that was bee

Re: [Freesurfer] (no subject)

The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit. -- On Fri, 4 Sep 2009, Kim, Miyoung wrote: > Hi. > > Just a quick question - is cortical

Re: [Freesurfer] (no subject)

Hi Miyoung", it's based on the white (yellow line) and pial surfaces. cheers, Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote: > Hi. > > Just a quick question - is cortical parcellation performed based on the pial > line (red line) or the cortical segmentation (brown shade)? The reason for > t

Re: [Freesurfer] (no subject)

So the segmentation and the cortical parcellation are completely independent? Or does the cortical parcellation still use information from the segmentation? Bruce Fischl wrote: > Hi Miyoung", > > it's based on the white (yellow line) and pial surfaces. > > cheers, > Bruce > > On Fri, 4 Sep 2009,

Re: [Freesurfer] (no subject)

Hi Anthony, mostly independent. The surface reconstruction itself is dependent on the subcortical labeling, and we do use the subcortical information for distinguishing callosum for cingulate and such, but otherwise they are independent. cheers, Bruce On Fri, 4 Sep 2009, Anthony Dick wrote: >

[Freesurfer] Windows VirtualBox freesurfer v4.5.0

For users wishing to run Freesurfer on Windows, there is now a VirtualBox instance of Ubuntu with freesurfer 4.5.0 installed available for download from the site: http://surfer.nmr.mgh.harvard.edu/fswiki/Download Note the link to README file which provides brief installation notes of the download

Re: [Freesurfer] Windows VirtualBox freesurfer v4.5.0

Thanks Nick! The link to download VirtualBox is: http://www.virtualbox.org/wiki/Downloads --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter

Re: [Freesurfer] (no subject)

Thank you Allison and Bruce for your feedback! Some follow-up questions if I may - are the volumes for the gray matter and the cerebellum as indicated in the aseg stats file reliable and thus usable (e.g. can we use the GM volume in the file if it's labeled as cerebellum/use the cerebellum volu

Re: [Freesurfer] (no subject)

Hi Miyoung, you can always edit the aseg.mgz if you want. Do you find this happens frequently? That hasn't been our experience. Bruce On Fri, 4 Sep 2009, Kim, Miyoung wrote: > Thank you Allison and Bruce for your feedback! > > Some follow-up questions if I may - are the volumes for the gray mat