[Freesurfer] info about ?h.cortex.label

Hello all, I recently noticed that one of the labels that appears to be standard output from recon-all is ?h.cortex.label. I can't seem to find any documentation about this label on the wiki, and I was hoping someone could tell me what exactly this label is (e.g. does it exclude the entire

[Freesurfer] interpret analysis results

First, thanks to Doug for all his help up to this point. Next, I have three questions. In my analysis, I used the -paired-diff and -osgm options in mris_preproc and mri_glmfit, respectively. I have successfully loaded sig.mgh onto the inflated surface. Are the values from the color chart

Re: [Freesurfer] info about ?h.cortex.label

Hi David, it's generated during the mris_make_surfaces deformations using the aseg, and is meant to exclude the entire medial wall as well as the bit of the basal ganglia that are in the insula Bruce On Mon, 22 Jan 2007, David Ziegler wrote: Hello all, I recently noticed that one of the

[Freesurfer] Longitudinal analysis

Hello users, Is there a typo on the longitudinal analysis page on the wiki.. does the command go like this?? recon-all-long -long -subjid tp1 -subjid tp2 Thanks Chacko. Expecting? Get great news

Re: [Freesurfer] interpret analysis results

The values are -log10(p), so p .01 would require a threshold of 2, etc. I don't use t, z, or F because I have not memorized the various tables that convert them to p:). The sig will map to any surface, including pial. doug Reschke, Cole wrote: First, thanks to Doug for all his help

RE: [Freesurfer] -noaseg

Kazu, This is for a non-human primate, right? If so, you will need to manually define seed points for the corpus callosum and pons. To do so, open the white matter volume in tkmedit: tkmedit subjid wm.mgz and using the cursor, identify the 'volume index' of the point where you think the

Re: [Freesurfer] single set without skull -- help

Yan, It looks like perl is installed (normally in /usr/bin) if you are getting an output from nu_correct. Can you send me your recon-all.log file? Also, what is the output when this is typed: which nu_correct Nick On Mon, 2007-01-22 at 11:50 -0800, yanxia wrote: Hello Nick, Sorry for

Re: [Freesurfer] Longitudinal analysis

Chacko, Which wiki page are you referring to? Recon-all-long is used like this: recon-all-long -long -tp1 tp1 -subjid tp2 ... where ... refers to what flags you want to use (like -all). Nick On Mon, 2007-01-22 at 10:35 -0800, Chacko Cherian wrote: Hello users, Is there a typo on the

Re: [Freesurfer] Longitudinal analysis

Sorry Nick,I dont seem to get it..it says recon-all-long:Command not found --- Nick Schmansky [EMAIL PROTECTED] wrote: Chacko, Which wiki page are you referring to? Recon-all-long is used like this: recon-all-long -long -tp1 tp1 -subjid tp2 ... where ... refers to what flags you

Re: [Freesurfer] Longitudinal analysis

recon-all-long is attached. to install, copy the attached file to your $FREESURFER_HOME/bin and type: gunzip recon-all-long.gz chmod a+x recon-all-long the longitudinal processing functionality contained in this script will be incorporated into recon-all in the next release. On Mon,

[Freesurfer] Freesurfer usage on Ubuntu 6.06

Hello All, I just installed Freesurfer, the Red Hat 9 version for Ubuntu 6.06. I followed all the instructions and made the changes as directed to my .bashrc and .bash_profile files to include the two lines as follows: export FREESURFER_HOME=/usr/local/freesurfer source

Re: [Freesurfer] Freesurfer usage on Ubuntu 6.06

Binyam, You will need to install tcsh on your system, as most of the freesurfer utilities use it. Nick On Mon, 2007-01-22 at 17:59 -0600, Binyam Nardos wrote: Hello All, I just installed Freesurfer, the Red Hat 9 version for Ubuntu 6.06. I followed all the instructions and made the changes