I would like to run FreeSurfer just up to the point it creates the aseg file, and no further. I believe this would be steps 1 through 11. Is there any way other than making a copy of the recon-all script and removing everything after step 11. Not sure I know exactly where this is.
-Jeff
Hi Jeff,
you can run recon-all with flags -autorecon1, -gcareg, -canorm, -careg, -careginv, -rmneck, -skull-lta and -calabel if you want to generate files upto aseg.mgz. Please refer to this wiki for more details about the flags.
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1
Sita.
On Mon, 1 Aug 2011, Jeff Eriksen wrote:
I would like to run FreeSurfer just up to the point it creates the aseg file, and no further. I believe this would be steps 1 through 11. Is there any way other than making a copy of the recon-all script and removing everything after step 11. Not sure I know exactly where this is.
-Jeff
I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files l&Rh.white and l&rh.pial. Can someone please confirm this, and also confirm that these are in the "triangle surface file" binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen
Yes, and we provide m files for reading them Cheers Bruce
On Sep 14, 2011, at 9:46 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:
I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files l&Rh.white and l&rh.pial. Can someone please confirm this, and also confirm that these are in the "triangle surface file" binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Super! Please tell me how to obtain the m-files. -Jeff
On 9/14/11 6:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Yes, and we provide m files for reading them Cheers Bruce
On Sep 14, 2011, at 9:46 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:
I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files l&Rh.white and l&rh.pial. Can someone please confirm this, and also confirm that these are in the "triangle surface file" binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
You should already have them. In your $FREESURFER_HOME dir there is a sub-dir called 'matlab'. I believe 'read_surf.m' is what you are looking for. -Louis
On Wed, 14 Sep 2011, Jeff Eriksen wrote:
Super! Please tell me how to obtain the m-files. -Jeff
On 9/14/11 6:49 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Yes, and we provide m files for reading them Cheers Bruce
On Sep 14, 2011, at 9:46 PM, Jeff Eriksen eriksenj@ohsu.edu wrote:
I wish to extract the pial and GW surfaces from their surface files to manipulate in Matlab. As far as I can determine, these are the files l&Rh.white and l&rh.pial. Can someone please confirm this, and also confirm that these are in the "triangle surface file" binary format? If this is all true, I can proceed to opening and reading the meshes. Thanks, -Jeff Eriksen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Jeff Eriksen -
Louis Nicholas Vinke -
Sita Kakunoori