Thanks for clarifying this Doug! Please let me know if anyone has suggestions about my other questions below, re skull stripping.
Cheers! T On 8 July 2013 18:01, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz > > If you only have one run, then 001 and raw are the same > orig.mgz is the first conformed volume > > doug > > > > On 07/08/2013 12:38 PM, Tudor Popescu wrote: > > Thanks Bruce. I have looked at that part of the wiki but I was > > wondering whether the screenshots at all suggest that all artefacts > > are likely to be the result of the same problem, and that e.g. > > re-running recon for all subjects with a watershed>25 and with the > > -no-wsgcaatlas flag might be the thing to do in this case, rather than > > manually editing slices in tkmedit. > > > > So after making these corrections to all affected subjects, before > > proceeding to analyses, is a visual inspection in freeview of the > > brain.mgz of all subjects enough? It seems like some of these > > skull-stripping errors are quite subtle and can be easily missed (as I > > have, in fact, when I checked the output after my first recon-all). > > > > the T1.mgz is intensity corrected and conformed (the orig.mgz is > > just conformed). > > > > So are both derived from 001.mgz? Otherwise, what is the difference > > between 001.mgz and orig.mgz? > > > > Thanks! > > Tudor > > > > > > _______________________________________________ > > 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 > > > 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. > >
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