Hi,
we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this but I can't seem to find it. Is there something still around ?
thanks
Greg.
Greg,
From the Data Requirements section of the beginners page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
there is a link to Andre Van der Kouwe's page on the scanner protocols used at the NMR Center:
http://www.nmr.mgh.harvard.edu/~andre/
Nick
On Tue, 2007-04-17 at 17:09 -0400, Kirk, Gregory wrote:
Hi,
we just got our 3T Siemens scanner and I was lookinging for the recomendations on sequence and protocoll parameters that are sugested for data acquisitions to give best results with freesurfer segmntation/cortical recon etc. It seems there was a web page that had the suggested best for this but I can't seem to find it. Is there something still around ?
thanks
Greg. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear surfers,
I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like :
mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon
it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by :
mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial
however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general.
In the help of mri_surf2vol for the fillribbon option, it is explained as "iterate projfrac from 0 to 1". And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels.
Thanks in advance.
Burak
Hi Burak,
I'm not really sure what you are trying to do, but a cortical ribbon is generated as part of the recon process, mri/?h.ribbon.mgz. Perhaps this is what you are looking for?
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of burak ozkalayci Sent: Wednesday, April 18, 2007 6:39 AM To: Freesurfer Mailing List Subject: [Freesurfer] Grainy thickness ribbon
Dear surfers,
I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like :
mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon
it generates a very grainy map. I think that those unassigned voxels are not hit by the normals of vertices on the white surface. To compensate it I tried to fill the ribon with the normals originated from the pial surface by :
mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon --surf pial
however the ribbon I get is shifted to the outer side of the cortex. I think the normals of the pial are oriented to show outer space of the cortex and they hit the voxels at the outerspace. I also attached the thickness maps of the ribbon I get from the white and the pial surfaces and the T1 image. They are the same slice of the volume, and you can see that pial one passes beyond the pial surface in general.
In the help of mri_surf2vol for the fillribbon option, it is explained as "iterate projfrac from 0 to 1". And when the code is running I saw that iteration has a 0.05 step. I wonder whether is it possible to define the stepsize and the range for example 0 to -1 to reverse the hitting voxels.
Thanks in advance.
Burak
freesurfer@nmr.mgh.harvard.edu
-
burak ozkalayci -
Jenni Pacheco -
Kirk, Gregory -
Nick Schmansky