[Freesurfer] (no subject)

Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all commands) take. thanks, Elina___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

[Freesurfer] (no subject)

Hello, Do you know how can I convert my images which are in ctf format to a freesurfer compatible format? thanks, Elina___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

recon-all -all will take approximately 30 hours. It depends on the quality of your data and how many errors need to be fixed. Allison -- On Wed, 29 Apr 2009, Elina Pitri wrote: Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all comm

RE: [Freesurfer] (no subject)

Hi Elina, You could have a look at http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Step-wiseDirectives-1 and http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable to identify the needed time of each process. But I have to mention, that the timeline is not perfectly accurate and can vary

[Freesurfer] longitudinal processing

FreeSurfers, I am using the longitudinal processing stream to look at change in the lateral ventricles at several timepoints. As a control measure, we are running two consecutive baseline images in the scanner. These images were done back-to-back, exactly the same, and the subject did not ge

[Freesurfer] corpus callosum segmentation

The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both 5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think they should not co-exist. Maybe I¹m wrong. Wayne ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] longitudinal processing

Hi Dana, we have uncovered a problem with the longitudinal stream that may account for this. We're hoping to have a fix in the near term. cheers, Bruce On Wed, 29 Apr 2009, Dana W. Moore wrote: FreeSurfers, I am using the longitudinal processing stream to look at change in the lateral v

Re: [Freesurfer] corpus callosum segmentation

you're probably right. We used to segement the cc on the surface, but this wasn't nearly as accurate as in the volume, which replaced it. cheers Bruce On Wed, 29 Apr 2009, Wayne Su wrote: The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both 5 parts along with ctx-?h-c

[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area

Hello, Here is my bugr info if you need it: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090428 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine:

Re: [Freesurfer] corpus callosum segmentation

Thank you Bruce, So, if I want to report the volume of the Corpus Callosum, I should add up the volumes of CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior only. The ctx-?h-corpuscalosum/wm-?h-corpuscallosum is just useless and better to remove them from wmparc.mgz since th

Re: [Freesurfer] corpus callosum segmentation

yes. On Wed, 29 Apr 2009, Wayne Su wrote: Thank you Bruce, So, if I want to report the volume of the Corpus Callosum, I should add up the volumes of CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior only. The ctx-?h-corpuscalosum/wm-?h-corpuscallosum is just useless and b

[Freesurfer] Surface area and curvature

What is the best reference regarding the calculation of surface area and surface curvature and are there any studies looking at the reliability of these measures? Thanks Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical

Re: [Freesurfer] Surface area and curvature

not that I know of. Bruce On Wed, 29 Apr 2009, Richard Frye wrote: What is the best reference regarding the calculation of surface area and surface curvature and are there any studies looking at the reliability of these measures? Thanks Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assi

[Freesurfer] mri_normalization, what do the command line switches do?

Aloha, fellow freesurfers, currently I am in the process of switching from freesurfer 3.0.5 to 4.3.0 (hopefully I can do the same for fsfast later). In that process I am revisiting mzy old scripts and try to improve them (or at least get rid of some cargo-cult coding). One of the more crirt

[Freesurfer] tksurfer question

Hi fellow Surfers, in 3.0.5 (Linux centos4_x86_64) I used to be able to the following from a subdirectory myscripts-anat in the subjects directory: tksurfer subjects_name lh inflated -overlay lh.sulc Now, on macosx 4.3.0 this does not work anymore. I get: ERROR: cannot find lh.sulc using: t

Re: [Freesurfer] Surface area and curvature

this reference may be relevant: Discrete Differential-Geometry Operators for Triangulated 2-Manifolds (Mark Meyer, Mathieu Desbrun, Peter Schröder and Alan H. Barr), VisMath 2002 the pdf is available at: www.multires.caltech.edu/pubs cheers, roberto On Wed, Apr 29, 2009 at 9:17 PM, Richard Frye