Hello all,
I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days).
It would be nice if the defects are handled separately of each other to parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each.
Best, Falk
Hi Falk
we usually don't process the .5mm data directly. Instead we "conform" it to 1mm iso, recon it, then run mris_make_surfaces posthoc directly on the .5mm data to nudge the surfaces around to agree with it.
Parallelizing mris_fix_topology is certainly possible if only we had an extra engineer to work on it....
cheers Bruce
On Wed, 16 Jan 2013, "Falk Lüsebrink" wrote:
Hello all,
I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days).
It would be nice if the defects are handled separately of each other to parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each.
Best, Falk _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
so you use the conformed and fixed ?h.orig during mris_make_surfaces on the .5mm data? Never thought of that.
Best, Falk
-------- Original-Nachricht --------
Datum: Wed, 16 Jan 2013 11:16:45 -0500 (EST) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: "Falk Lüsebrink" falk.luese@gmx.net CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Speeding up mris_fix_topology
Hi Falk
we usually don't process the .5mm data directly. Instead we "conform" it to 1mm iso, recon it, then run mris_make_surfaces posthoc directly on the .5mm data to nudge the surfaces around to agree with it.
Parallelizing mris_fix_topology is certainly possible if only we had an extra engineer to work on it....
cheers Bruce
On Wed, 16 Jan 2013, "Falk Lüsebrink" wrote:
Hello all,
I'm processing some high resolution data with an isotropic resolution of
0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days).
It would be nice if the defects are handled separately of each other to
parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each.
Best, Falk _______________________________________________ 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.
yes On Wed, 16 Jan 2013, "Falk Lüsebrink" wrote:
Hi Bruce,
so you use the conformed and fixed ?h.orig during mris_make_surfaces on the .5mm data? Never thought of that.
Best, Falk
-------- Original-Nachricht --------
Datum: Wed, 16 Jan 2013 11:16:45 -0500 (EST) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: "Falk Lüsebrink" falk.luese@gmx.net CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Speeding up mris_fix_topology
Hi Falk
we usually don't process the .5mm data directly. Instead we "conform" it to 1mm iso, recon it, then run mris_make_surfaces posthoc directly on the .5mm data to nudge the surfaces around to agree with it.
Parallelizing mris_fix_topology is certainly possible if only we had an extra engineer to work on it....
cheers Bruce
On Wed, 16 Jan 2013, "Falk Lüsebrink" wrote:
Hello all,
I'm processing some high resolution data with an isotropic resolution of
0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days).
It would be nice if the defects are handled separately of each other to
parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each.
Best, Falk _______________________________________________ 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@nmr.mgh.harvard.edu
-
"Falk Lüsebrink" -
Bruce Fischl