Hi again, I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions!
Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu <tud...@gmail.com> wrote: > Thanks Bruce. So the massive chunks that appear as missing in freeview, > e.g. at coronal slice 153, show correctly in tkmedit, although the surfaces > don't exist there. If I mouse above that area, brainmask.mgz intensities > (which seem to be always identical to T1.mgz ones) seem quite normal to me, > i.e. they're not all 0 but vary in a range centred around ~100. > > As for the segmentation (aseg) - not quite sure where I need to look for > that. I attach here the main volumes & surfaces of this subject. Could my > "-wsthresh 35" recon not have replaced the existing one? > > Many thanks again! > Tudor > > PS: why does freeview show the coordinates in the order [x z y] instead of > [x y z]? I.e., as I move from anterior to posterior, I'd expect the middle > coordinate to decrease, rather than the third one. > > PPS: what is the difference between brain.mgz and brainmask.mgz? Is it to > do with conformity and intensity correction, just like the difference > between 001.mgz and T1.mgz? I would have thought that brainmask.mgz would > be a binary image (a mask consisting of 0s and 1s), rather than a regular > (skull-stripped) structural. > > > On 11 July 2013 21:40, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Tudor >> >> can you cc the list so others can answer? What are the intensities in the >> excluded right temporal wm in the brainmask.mgz? What is the aseg like >> there? Looks like an intensity normalization failure, but I'm not sure why. >> If you want to upload the subject I'll take a look >> Bruce >> >> On Thu, 11 Jul 2013, Tudor Popescu wrote: >> >> Hi Bruce, >>> >>> Sorry, wasn't sure whether you'd seen my previous message. So in the >>> meantime, after the following command for subject C06 (whose artefactual >>> skull strip I previously included as a screenshot) completed without >>> error, >>> >>> recon-all -skullstrip -wsthresh 35 -clean-bm -subjid C06 >>> >>> ..the volumes&surfaces still look bad (see screenshot and recon log >>> attached). >>> >>> C06 is just one of several subjects for which this has happened. Is there >>> anything else I can try? Thanks! >>> >>> Tudor >>> >>> On 9 July 2013 13:33, Tudor Popescu <tud...@gmail.com> wrote: >>> 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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<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/<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<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<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.
