Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
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Sasha,
Yes you would need to re-run mris_make_surfaces if 'setenv FIX_VERTEX_AREA' was not set.
FYI, later today, v3.0.1 of stable freesurfer will be posted, which includes the fix to the two known issues, one being the removal of the need to set FIX_VERTEX_AREA in your env.
Nick
On Mon, 2006-03-13 at 13:56 -0500, Sasha Wolosin wrote:
Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
If you ran it outside of recon-all then you should re-run it. Sorry.
On Mon, 13 Mar 2006, Sasha Wolosin wrote:
Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but I forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I saved a back-up of the surf folder created by recon-all. Will I need to re-run mris_make_surfaces? Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Regarding stable 3.0.1: Have there been any changes in recon-all processing? i.e. Should I re-run subjects processed with recon-all in stable 3 if I want to upgrade to stable 3.0.1? Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 3/13/2006 5:00 pm >>>
If you ran it outside of recon-all then you should re-run it. Sorry.
On Mon, 13 Mar 2006, Sasha Wolosin wrote:
Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but
I
forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I
saved a
back-up of the surf folder created by recon-all. Will I need to
re-run
mris_make_surfaces? Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sasha,
There is no need to re-run subjects processed with stable v3.0. The only difference from stable v3.0 is that it is no longer necessary to set FIX_VERTEX_AREA in the env if using utilities outside of recon-all.
Nick
On Mon, 2006-03-13 at 18:45 -0500, Sasha Wolosin wrote:
Regarding stable 3.0.1: Have there been any changes in recon-all processing? i.e. Should I re-run subjects processed with recon-all in stable 3 if I want to upgrade to stable 3.0.1? Thanks, Sasha
Doug Greve greve@nmr.mgh.harvard.edu 3/13/2006 5:00 pm >>>
If you ran it outside of recon-all then you should re-run it. Sorry.
On Mon, 13 Mar 2006, Sasha Wolosin wrote:
Dear all, I ran the 'mris_make_surfaces' script after running recon-all, but
I
forgot to include 'setenv FIX_VERTEX_AREA' in my set up file. I
saved a
back-up of the surf folder created by recon-all. Will I need to
re-run
mris_make_surfaces? Thanks, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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freesurfer@nmr.mgh.harvard.edu
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Nick Schmansky -
Sasha Wolosin