I have 2 questions related to version 4.1.
1) The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not updated to reflect the new steps in version 4.1. Does anyone have a breakdown of these new steps? I was not sure of the flags for these new steps, or where they fit in (are they part of 2-pial, 2-cp or 3?) Is the wiki going to be updated to reflect this new version?
2) When I load an image in tkmedit (after it has been run all the way through step 3) I get an error message and it won't load the aseg. The aseg is there, I just have to load it manually. Did the following flag change with the new version?
brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white - segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Thanks.
KT LaBadie
Hi KT,
for 2) the usage changed, and you don't need to specify mri (i.e. -segmentation aseg.mgz). For 1), which new steps do you mean specifically?
Bruce On Fri, 19 Oct 2007, Kt Labadie wrote:
I have 2 questions related to version 4.1.
- The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not updated
to reflect the new steps in version 4.1. Does anyone have a breakdown of these new steps? I was not sure of the flags for these new steps, or where they fit in (are they part of 2-pial, 2-cp or 3?) Is the wiki going to be updated to reflect this new version?
- When I load an image in tkmedit (after it has been run all the way through
step 3) I get an error message and it won't load the aseg. The aseg is there, I just have to load it manually. Did the following flag change with the new version?
brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Thanks.
KT LaBadie
It´s 4.0.1 or 4.1?
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Kt Labadie Sent: sexta-feira, 19 de outubro de 2007 15:36 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Version 4.1 questions
I have 2 questions related to version 4.1.
1) The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not updated to reflect the new steps in version 4.1. Does anyone have a breakdown of these new steps? I was not sure of the flags for these new steps, or where they fit in (are they part of 2-pial, 2-cp or 3?) Is the wiki going to be updated to reflect this new version?
2) When I load an image in tkmedit (after it has been run all the way through step 3) I get an error message and it won't load the aseg. The aseg is there, I just have to load it manually. Did the following flag change with the new version?
brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Thanks.
KT LaBadie
Hi,
I can get all the ponits of the cortical surface in ascii format. Anyway I can plot the contour of the 3D surface on a plane? I tried to find all the points in one plane, but the order is not along the contour line. I can only plot the surface as "dots", instead of "lines" in a 2D plane. I am wonderng how "tkmedit" plots the surface lines. Any freesurfer function can do this? Thanks.
XJ Kang
tkmedit finds ever triangle that intersects the viewing plane then computes the closed contour connecting them. Is that what you want?
Bruce
On Fri, 19 Oct 2007, XJ Kang wrote:
Hi,
I can get all the ponits of the cortical surface in ascii format. Anyway I can plot the contour of the 3D surface on a plane? I tried to find all the points in one plane, but the order is not along the contour line. I can only plot the surface as "dots", instead of "lines" in a 2D plane. I am wonderng how "tkmedit" plots the surface lines. Any freesurfer function can do this? Thanks.
XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Kt Labadie -
Pedro Paulo Oliveira Jr -
XJ Kang