[Freesurfer] aseg.mgz altered after auto-recon2?
Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours. recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8 cheers, Natalie On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
nope, you wouldn't benefit any further I don't think On Thu, 28 Mar 2013, Joshua Lee wrote: Hey thanks, I haven't worried about multi threading typically since I just run more brains simultaneously. On my computer, I have sufficient 64 gigs RAM (64 gigs) and 24 CPU/cores (not sure which) to run 20 recon-all scripts simultaneously at full speed. Would I still benefit from the multi threading? I am a little confused about cores vs cpus I created a copy of the recon-all script that stops at calabel step, and am running that now. - Josh On Thu, Mar 28, 2013 at 12:58 PM, Natalie Han zh...@stanford.edu wrote: Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours. recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8 cheers, Natalie On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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 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.
