[Freesurfer] Normalization problem

I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control p

Re: [Freesurfer] Normalization problem

Hi Martin, we're looking into it - it's probably a bug in recon-all. Bruce On Mon, 21 Nov 2005, Martin Ystad wrote: I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogene

[Freesurfer] warning

Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e

[Freesurfer] Freesurfer mailing list and google

Dear freesurfer users, By adding the following phrase to google's search box, you can search the freesurfer mailing list archives. site:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ I have found this extremely useful. Satra ___ Freesurfer

Re: [Freesurfer] warning

don't worry about it - we're taking it out. Bruce On Mon, 21 Nov 2005, Sasha Wolosin wrote: Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The mater

[Freesurfer] mri_convert problem?

I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/parameter_maps_average/average_bet.img /space/windu/4/users/recon/GORG25_recon/mri/32echo/magnitude/

RE: [Freesurfer] Normalization problem

Hi, I've encountered similar problems. Do you know if it's specific to the autorecon2 flag? I'm wondering if running each process separately and sequentially get around it, e.g, running recon-all -normalization2, then recon-all -segmentation, then recon-all -fill, etc... Thanks, Alex Alex F

Re: [Freesurfer] mri_convert problem?

does the output dir exists? Do you have write permission? On Mon, 21 Nov 2005, Daniel Goldman wrote: I've been getting this error message whenever I try to convert to .mgz format: mri_convert /space/windu/4/users/recon/GORG25_recon/mri/32echo/magni