[Freesurfer] Volume estimates i Freesurfer

Members How do I get the actual numbers for the structural volumes after I have done the cortical and subcortical segmentations? Is the "norm" command needed to get the correct values? What are the units (ml or qubic cm/mm)? Is it possible to get a printable list? Thanks Kjell-Inge Gjesd

[Freesurfer] -notalairach error?

Hi, I have just realized I made a mistake when I ran recon-all -s subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is overridden by autorecon1. Nevertheless, when I look at the dates of the files, I see that talairach.xfm is the one I edited, although talairach.log has a poste

[Freesurfer] mri_convert problem

I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subjects directory to /home/amc/freesurferstable/subjects, which is where my first data set is located, /1593-4. First I ch

Re: [Freesurfer] mri_convert problem

to convert Dicom files to mgz try to use following: mri_convert -it dicom -i dicom_file -o your_file.mgz to get more options type mri_convert -- help Silvester [EMAIL PROTECTED] wrote: I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some v

Re: [Freesurfer] mri_convert problem

try running it with -debug and send along the output. cheers, Bruce On Mon, 12 Jun 2006 [EMAIL PROTECTED] wrote: I am trying to convert Dicom files to mgz format and I keep getting the same error even when I try some variations on what I am typing in the terminal. I have already set my subje

Re: [Freesurfer] mri_convert problem

Dave, It looks like a version of recon-all from 2004 is being used, which predates the -i flag. Have you installed the newest version of freesurfer (v3.0)? Or use mri_convert to create the 001.mgz, 002.mgz input files in your /mri/orig directory, and run recon-all from there. Nick > I am tryin

[Freesurfer] error message

I was running the subcortical labelling script (aseg_rerun.csh) using the old version of freesurfer, and have received this error message: mri_read(): couldn't determine type of file mri_ca_register: could not open input volume -T I am not sure how to fix this error.  I would appreciate any input!!

[Freesurfer] neighborhood of a vertex

Hi, I convert a thickness file to ascii format and the file looks like   (vertex id, x, y, z, thickness) 000 -36.19709 -19.27060 66.10529 2.61633 001 -16.37191 -69.16402 59.60456 2.18290 002 -10.58665 -10.65137 50.24026 2.06269 003 -22.09574 43.85081 28.52032 1.54455 004 -57.95597 -0.45362

[Freesurfer] License

I'm confused about how to use my license key. It was sent to me, but there isn't a file names .license in my freesurfer home folder. And there isn't a license key FILE, only the three lines of text sent to me. What should I type in the command line to validate the license? __

Re: [Freesurfer] License

Create a new file inside your freesurfer directory called .license and copy those three lines into the file. On Mon, Jun 12, 2006 at 02:31:15PM -0400, [EMAIL PROTECTED] wrote: > I'm confused about how to use my license key. It was sent to me, but > there isn't a file names .license in my freesu

Re: [Freesurfer] neighborhood of a vertex

Hi Ron, convert one of the surfaces to ascii as well. It contains both a list of vertices (like the thickness) and a list of triangles, which has the nbhd info you need. cheers, Bruce On Mon, 12 Jun 2006, R. Chen wrote: Hi, I convert a thickness file to ascii format and the file looks like

Re: [Freesurfer] License

you should just put them in a file named .license in the FREESURFER_HOME directory. Bruce On Mon, 12 Jun 2006 [EMAIL PROTECTED] wrote: I'm confused about how to use my license key. It was sent to me, but there isn't a file names .license in my freesurfer home folder. And there isn't a licens

[Freesurfer] inflated surface not seen

Hi all, I've run recon-all -autorecon1 and -autorecon2, successfully. But when I opened inflated surface using tksurfer, only a tiny bit of image of the inflated surface was seen. Something was wrong in the process. Both wm, filled, brain volumes looked OK. Here is the data on the web; http://www

[Freesurfer] smoothing

Hi, In the --help output of mri_surf2surf, the following explanation is given for --fwhm-src fwhmsrc:     Smooth the source or target with a gaussian with the given fwhm (mm). This is     actually an approximation done using iterative nearest neighbor smoothing.     The number of iterations is com

Re: [Freesurfer] smoothing

Hi Lars, I think the formula is: fwhm = (2.3*sqrt(niter*2/pi)); Doug's in Florence, so may not reply right away. I think there's also a correction for the average surface as it has less surface area than any of the subjects in the average. cheers, Bruce p.s. here's the code snippet from mr

RE: [Freesurfer] neighborhood of a vertex

From: "R. Chen" <[EMAIL PROTECTED]> To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] neighborhood of a vertex Date: Mon, 12 Jun 2006 11:02:59 -0700 (PDT) I want to do some customrized smoothing and need to know the neighborhood of a vertex. I think FreeSurfer also uses this neighborhoo

RE: [Freesurfer] neighborhood of a vertex

thanks Don, one warning: Doug implemented Moo Chung's smoothing and we didn't find quite the same results he reported. There seemed to be some scale factor that was off (that is, the relationship between fwhm and iterations of diffusion smoothing wasn't quite right). Thanks for posting this