Re: [Freesurfer] Question about mri_ca_normalize

Hi John, do you want to send us a sample dataset so we can take a look? Bruce On Mon, 13 Oct 2008, John Sheppard wrote: Hey Freesurfers, Couple question about 2 FS commands: first is mri_normalize, a command used in -autorecon2 pipeline. 1) Can someone tell me exactly what flags to pass thi

[Freesurfer] Question about mri_ca_normalize

Hey Freesurfers, Couple question about 2 FS commands: first is mri_normalize, a command used in -autorecon2 pipeline. 1) Can someone tell me exactly what flags to pass this command in order for it to be as aggressive as possible in bumping up intensities, in an attempt to end up with more expande

[Freesurfer] recon-all with voxel sizes other than 1mm^3

Dear all, Is there a way to have all the results from recon-all in the native image space (in our case, 0.8x0.8x0.8mm), rather than conformed to 1mm^3? Looking at the script, I'm worried that replacing the --conform to --noconform option to mri_convert may prevent the downstream steps to work c

[Freesurfer] recon-all with voxel sizes other than 1mm^3

Dear all, Is there a way to have all the results from recon-all in the native image space (in our case, 0.8x0.8x0.8mm), rather than conformed to 1mm^3?Looking at the script, I'm worried that replacing the --conform to --noconform option to mri_convert may prevent the downstream steps to work correc

Re: [Freesurfer] Topology fixer

Hi Juergen, Florent Segonne implemented a newer topology correction that I believe we use in cases where the old one failed. cheers, Bruce On Mon, 13 Oct 2008, Juergen Haenggi wrote: Dear FS experts I am wondering why there is a special kind of topology fixing (see attachment) in one of m

Re: [Freesurfer] Creating template rat model

Hi Martin (and others), This worked! Great thanks. However, when I come to the skull-stripping sequence I get the message that WM values are lower than CSF. In some way this doesn't make sense, but when considering the T1.mgz file. It becomes clear from the segmentation it can be seen that the

Re: [Freesurfer] Creating template rat model

Mark, without prior knowledge of what you do, I can just recommend you the recon-all option "-notal-check". You can find out more about it by running "recon-all -help | less". So your command would look like: recon-all -autorecon1 -notal-check -s $YOURRAT Best, Martin On Monday 13 October 2

[Freesurfer] Creating template rat model

Hi, I'm trying to create a template model for rats. I've learned through the surface registration template (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that I have to run the recon-all procedure at least once. However when I run the recon-all -autorecon1 option it stops at

[Freesurfer] Topology fixer

Dear FS experts I am wondering why there is a special kind of topology fixing (see attachment) in one of my subjects, but not in the other subjects. Why there is a different FS output in that subject? What does it mean? Should I exclude this subject? Thanks in advance Regards Juergen

[Freesurfer] Re: Freesurfer Digest, Vol 56, Issue 20

Hi All, On Oct 11, 2008, at 11:23 PM, [EMAIL PROTECTED] wrote: Message: 4 Date: Sat, 11 Oct 2008 15:54:05 -0500 From: "Richard Frye" <[EMAIL PROTECTED]> Subject: [Freesurfer] qdec -- Cannot allocate memory To: freesurfer@nmr.mgh.harvard.edu Message-ID: <[EMAIL PROTECTED]> Content-Typ