Re: [Freesurfer] hyperintense artifact causing problems for segmentation

wow, that is noisy. Looks like the bright ring is dura. This isn't gado enhanced, is it? You could try using the gcut stuff On Tue, 12 Apr 2011, Sarah Whittle wrote: Hi, I'm working with some poor quality images and having a lot of trouble with FreeSurfer segmentation. The main issue is

[Freesurfer] Error downloading old version of freesurfer

Hi, When I try to download an old version of freesurfer (4.3.1) from http://www.freesurfer.net/pub/dist/freesurfer/4.3.1/ I get the following error message: The connection was reset The connection to the server was reset while the page was loading. I get the same error message with all

Re: [Freesurfer] bbregister

that looks like it is the right command-line. Can you send the terminal output? Saad Ramadan wrote: Hi freesurfer-ers: when you run something like: * bbregister --s MySubject --t1 --mov t1_svs.nii --init-fsl --reg t1.reg.dat * * * I expect to generate a file t1.reg.dat.

[Freesurfer] Segmentation Fault

Hi All, Upon trying to assembly my subjects into a single surface space, I got the following error: *ERROR: number of vertices in /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness does not match surface (142271,140585) ERROR: reading curvature file * I then tried to perform recon-all

Re: [Freesurfer] Segmentation Fault

Hi Allie, what do you mean by trying to assemble my subjects into a single surface space? thanks Bruce On Tue, 12 Apr 2011, Allie Rosen wrote: Hi All, Upon trying to assembly my subjects into a single surface space, I got the following error: *ERROR: number of vertices in

[Freesurfer] Dura, manual editing, mri_gcut

Hi all, Sorry for the newbie questions, but I was wondering if there were any general guidelines on how much remaining DURA MATER and ARACHNOID MATER is acceptable after running autorecon1. In general, should dura be completely removed and arachnoid be left as is? Also, is mri_gcut run

[Freesurfer] fill problem in properly normalized volume

Dear all we have had some odd behavior in 4 fairly high quality datasets that have been very nicely normalized and deskulled with a good Talairach but then only half filled in wm.mgz and all surfs (to various semi-planes). Orientation seems correct in tkmedit as well. We were thinking that it

Re: [Freesurfer] Dura, manual editing, mri_gcut

Hi Roger, you certainly don't need to remove all of it - only the pieces that are erroneously retained within the pial surface. As for gcut, it depends on what version you are using whether it is run automatically. cheers Bruce On Tue, 12 Apr 2011 roger@yale.edu wrote: Hi all, Sorry

Re: [Freesurfer] fill problem in properly normalized volume

Hi Fred, do you want to send us an example set and we'll track it down? What version are you running? I suspect there is some old piece of code that Marty wrote that is at fault. cheers, Bruce On Tue, 12 Apr 2011, Fred Dick wrote: Dear all we have had some odd behavior in 4 fairly high

Re: [Freesurfer] Segmentation Fault

It usually means that you have a subject whose surfaces are out-of-synch. This usually happens when you've made edits, launched recon-all, but then then recon-all does not finish for some reason. Check the time stamps on that subject or try running recon-all -make all -s subject doug btw, a

Re: [Freesurfer] Segmentation Fault

Hi Doug, I read this on a previous email, and I already tried to run recon-all -make all. I included it in my original email, but I'll copy it here: I then tried to perform recon-all -make all, but got this error: *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log* In the .log, I got

Re: [Freesurfer] fill problem in properly normalized volume

Hi Bruce Believe it or not, we are running stable 5.0.0 (!). Since emailing I wised up and consulted recon all dev table for files - the first sign of trouble is in aseg.auto_noCCseg.mgz. The wm.seg.mgz is fine. I can upload a sub to incoming if you want to take a look Sorry didn't check

Re: [Freesurfer] fill problem in properly normalized volume

no worries, and I'm happy to take a look (although in general not as happy as I am to blame Marty) Bruce On Tue, 12 Apr 2011, Fred Dick wrote: Hi Bruce Believe it or not, we are running stable 5.0.0 (!). Since emailing I wised up and consulted recon all dev table for files - the first

[Freesurfer] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School

Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Job Description A postdoctoral position is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated

[Freesurfer] Bug in mri_info?

Freesurfers -- This morning, I was trying to convert a 4 frame MPRAGE scan into a 1 frame RMS image. I wrote my own matlab code to do it ... function err = rms_mprage(old,new) %convert 4-frame mprage into 1 frame mprage by taking RMS of voxels old_hdr = load_nifti(old); new_hdr = old_hdr;

[Freesurfer] Shifting hdr information in .nii?

A little off-topic maybe, but: I am working to load external data into analysis programs using .nii format files. I have inplanes acquired at an ACPC orientation, as well as data collected and specially pre-processed through a MATLAB pathway that unfortunately strips away all orientation

Re: [Freesurfer] hyperintense artifact causing problems for segmentation

I'll leave that for Nick, or one of the gcut developers. cheers Bruce On Wed, 13 Apr 2011, Sarah Whittle wrote: Thanks for your reply. I guess it could be dura. Here's a picture pre FreeSurfer with skull on. This is a particularly bad image. No, it's not gado enhanced. gcut is