Hi Bruce, What about the voxels having value equal to 5 (if exists) ?
Gunjan On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam <gunjan.gemin...@gmail.com> wrote: > Ok thank you Bruce > On Nov 23, 2014 10:37 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > >> we don't have a binary one, but all voxels in brainmask.mgz that are >5 >> are in brain and everything <5 is not in brain >> >> cheers >> Bruce >> >> On Sun, 23 Nov 2014, Gunjan Gautam wrote: >> >> >>> Thanks, >>> >>> And what about the binary brain mask? I am able to see only the stripped >>> volume but need the binary brain mask as well. >>> >>> Gunjan >>> >>> On Nov 23, 2014 8:49 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Gunjan >>> >>> 15 min is about what it is going to take. You could do it faster >>> but then the failure rate would go up. We've tuned it to improve >>> automaticity and reduce failures quite a bit. >>> >>> cheers >>> Bruce >>> >>> >>> On Sat, 22 Nov 2014, Gunjan Gautam wrote: >>> >>> >>> Hi, >>> >>> I used recon-all with all and its taking a lot of >>> time. My main concern is >>> only to get the stripped brain. >>> I tried with autorecon1 as well but its also taking >>> not less than 15min and >>> I need to deal with a huge data. >>> Last stage of autorecon1 is skull stripping which >>> takes the NU corrected >>> input (as it FS works as a pipeline). Is there any >>> way to directly get the >>> "stripped brain" and its binary mask. >>> >>> I also need to ask, which file of the output (name >>> with extension) is the >>> "binary brain mask" ? >>> >>> Best regards, >>> Gunjan >>> >>> >>> >>> _______________________________________________ >>> 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. >> >>
_______________________________________________ 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.
