Re: [Freesurfer] Probabilistic white matter mask

om: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, March 01, 2012 10:39 AM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Probabilistic white matter mask Hi Vanessa, I'm saying if you extract the white matter segmentation, then erod

Re: [Freesurfer] Probabilistic white matter mask

Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155 -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, March 01, 2012 10:21 AM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Probab

Re: [Freesurfer] Probabilistic white matter mask

Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155 -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, March 01, 2012 10:02 AM To: Palzes, V

[Freesurfer] Probabilistic white matter mask

I found a couple older threads about creating a probabilistic mask in Freesurfer: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/014953. html I have modified mri_ca_label with the flag -write-probs and inste

[Freesurfer] mri_binarize VS mri_extract_label

Could someone please explain to me the difference between mri_binarize and mri_extract_label? I had been using mri_extract_label to create ROI masks of cerebral white matter (2 and 41). I recently became aware that this would give me a label with 0 and 128. I tried mri_binarize (with the same matc

[Freesurfer] Segmentation fault during -autorecon1

Hello, I am continuously getting a "Segmentation fault" error during -autorecon1 when it's running mri_binarize. I have been running Freesurfer on a Mac, but now I am trying to implement it using Linux. I am running this version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on Linux 2.6.9-

Re: [Freesurfer] bert functional data set

-- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2011 1:12 PM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bert functional data set Hi Vanessa, you have to use some sort of template volume. I'm not sure what SPM uses as t

Re: [Freesurfer] bert functional data set

Tel: 415-221-4810 ext. 6155 -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, April 07, 2011 12:40 PM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bert functional data set That tutorial is out of date. Try using

[Freesurfer] bert functional data set

Hi, I'm trying to go through this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio nSpm I have already downloaded/unpacked the buckner_data-tutorial-subjs.tar.gz, and also set up the correct SUBJECTS_DIR as: setenv TUTORIAL_DATA /Applications/freesurfer/subjects

[Freesurfer] Mapping segmentations to SPM Functional Space

I am wondering if there is a similar function as aseg2feat (which maps the automatic segmentations from Freesurfer to FSL FEAT functional space) for the use in SPM functional analysis. This tool poses to be very useful in creating ROI masks, however, we are using SPM for functional analysis rather

[Freesurfer] Nu_correct error

Hi all, I've been consistently getting a couple of different errors early on during -autorecon1: .ncvarput: ncid 4: Bad file descriptor mivarput1: MINC package entry point sharpen_volume: crashed while running minclookup (termination status=768) nu_estimate_np_and_em: crashed while runni

[Freesurfer] ROI mask

Hi all, I am currently exploring anatomical ROI analysis in FreeSurfer. I would like to create ROIs based on a Brodmann Area atlas, since unfortunately FreeSurfer currently only segments a few of these regions automatically. I know I could define the ROI manually in FreeSurfer, but I would pref