you have to do the whole thing On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote: > Do I have to run recon-all entirely in order to extract volume for a > few Brodmann's areas? Or is there a way of optimizing the process by > striping it of any unneeded calculations? > > It is taking 21h to analyze one subject. > > Best, > luis > > 2015-12-22 9:44 GMT+11:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > If you're doing anatomical analysis, then FSFAST is not needed > (nor its > directly structure). If you have an input anatomical volume in any > format, then just run > > recon-all -s yoursubjectname -all -i inputfile > > inputfile can include img but be warned that img does not have > information about head orientation. This may cause a catastrophic > failure (eg, the head is upside down). If the head is left-right > reversed, then it probably won't fail but everything will be > left-right > reversed. don't say I did not warn you:) > > > On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote: > > > > Dear Douglas, > > > > It's an anatomical analysis. Perhaps I misunderstood the requirement > > for setting up the directories in the FSFAST for the recon-all > command. > > > > If that is the case, it is then a matter of converting my img files > > into mgz and run recon-all on them, am I right? > > > > Does the command recon-all also gives me volumes for specific > > Brodmann's areas? Or do I have to run a labeling to that? > > > > > > Thank you, > > > > luis > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
