[Freesurfer] Version 4.0.3 download

Hi there Apologies if this has been asked before, or is obvious. One of our machines has FreeSurfer version 4.0.3, and I would like to install the same version on another machine, but its a different architecture. Please can anyone tell me if, or where I can find the downloads for version 4.0

[Freesurfer] Segmentation errors

Hello all, We've noticed some errors in the wm and pial segmentations (see t1.png) even though the wm.mgz seems to be correct (see wm.png). Could you advise us on the best way to correct these errors? Many thanks, Nicola -

[Freesurfer] editing masks

Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill th

Re: [Freesurfer] Version 4.0.3 download

Matt, I've posted that release here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/rh9 Let me know if you need other ones. I'm hoping to get some bigger disks so we can put all of the old releases in one place. Nick On Tue, 2008-08-05 at 12:06 +0100, Matt Clarkson wrot

[Freesurfer] Floating exception (core dumped)

Hi, Running fsv405 on RHEL4 (64bit) and have encountered the following error after executing recon-all -all: Floating exception (core dumped). Did not encounter this error using fsv401 on the same box. See below for the standard output to screen. Any ideas? Many Thanks, Jenifer [EMAIL PROTECT

Re: [Freesurfer] Floating exception (core dumped)

Jenifer, Can you email me the recon-all.log file? From the output below, its not clear to me which binary is core dumpimg. Does recon-all continue normally? Nick On Tue, 2008-08-05 at 11:51 -0500, Juranek, Jenifer wrote: > Hi, > Running fsv405 on RHEL4 (64bit) and have encountered the followin

Re: [Freesurfer] segmentation errors

Hi Nicola, Its hard to tell from this one slice. My experience is that if you look on the wm.mgz volume up and back a few slices you'll notice a slice where there are edits to be made! Jenni On Tue, Aug 5, 2008 at 9:07 AM, Nicola Hobbs <[EMAIL PROTECTED]>wrote: > Hello all, > > We've noticed so

[Freesurfer] NITRC website

Of potential interest to people on this list is the NITRC website: http://www.nitrc.org/ "The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is funded by the National Institutes of Health Blueprint for Neuroscience Research. NITRC facilitates finding and comparing neuroi

Re: [Freesurfer] segmentation errors

hard to tell from a single slice, but my guess would be that there is a topological problem with the wm.mgz that you need to fix manually. Feel free to send it to us if you can't figure it out. cheers, Bruce On Tue, 5 Aug 2008, Nicola Hobbs wrote: Hello all, We've noticed some errors in th

Re: [Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

Hi Ian, does this mess up the ?h.white or ?h.pial surfaces? Or the aseg.mgz? If not, I wouldn't worry about it. cheers, Bruce On Tue, 5 Aug 2008, Ian Malone wrote: To illustrate the issue, this is a slice from one of the problematic volumes. The blue outlines surround non-zero voxels, the re

Re: [Freesurfer] editing masks

Sorry, I don't understand. Where did you get the mask? Or are you trying to create it from scratch? On Tue, 5 Aug 2008, Daniel H Choi wrote: Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I w

Re: [Freesurfer] Freesurfer Help

Hi Luke, we're rerunning all the tutorial data to recreate the snapshots and tutorials, since things have changed since we wrote them (and most of the things that used to fail no longer do!). cheers, Bruce On Fri, 1 Aug 2008, Luke Tseng wrote: To whom it may concern. We've been working w