Hi Derin we replace all 255s with 254 I think and 1 with 5 or something like that. I'd have to go dig up the code. If you add 110 it will work, but if you rerun it will not be retained.
cheers Bruce On Wed, 5 Feb 2014, Derin J Cobia wrote: > Could you clarify this a little more Bruce? I was under the same impression > as Ed that 110s could be used in editing the wm volume (but cannot recall > why/how I know that). We've edited using 110s and 255s with some limited > success for both (rerunning occasionally deletes these manual edits or > surface does not follow them) - maybe it is related to the mixing of > intensities? In a sense does using 110s trigger the stream to think a control > point was placed there (absent the Voronoi diagram, etc)? > > So, if manual 255s are always used, how are they differentiated from > ventricle or internal capsule ones? Does this even matter? Broadly, does > using a variety of intensity values affect other volumes (e.g. aseg, > brainfinalsurfs, etc)? > > Thanks, > Derin > > > On Feb 4, 2014, at 11:25 AM, Bruce Fischl <[email protected]> wrote: > >> Hi Ed >> >> it was never the case that an edited on wm.mgz voxel had the value of 110. >> It was always 255. 110 is the value that locations have when they are either >> an automatically or manually added control point >> >> cheers >> Bruce >> On Tue, 4 Feb 2014, Ed Gronenschild wrote: >> >>> Hi Martin, >>> One thing I want to be sure of: >>> should the edited wm voxels really have a value of either 1 or 255. >>> In previous versions an added wm voxel had a value of about 110, >>> this is not anymore the case? >>> I'm asking this because I want to edit wm by using results from another >>> application that segments wm, so not by means of manually editing >>> with freeview. >>> Cheers, >>> Ed >>> On 4 Feb 2014, at 17:00, Martin Reuter wrote: >>> >>> Hi Ed, >>> take a look at this wiki page about edits in the long stream: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits >>> everything should work. for long, you'd edit the base. If that is not >>> sufficient, you can edit the cross or the long. Edits from the cross >>> should be transferred to the long, except if the long already contain >>> manual edits. >>> Best, Martin >>> On Feb 4, 2014, at 9:06 AM, Ed Gronenschild >>> <[email protected]> wrote: >>> >>> Hi Bruce, >>> >>> When I have a look in the recon-all script I see that it >>> is tested if >>> there >>> are voxels present in wm.mgz with value 1 or 255. Both >>> indicate >>> wm editing. The comment in recon-all says that 1 means >>> remove >>> and 255 means add. >>> And concerning my second question: are these edited voxels >>> correcly processed with the option autorecon2-wm and >>> subsequently >>> with longitudinal processing? >>> >>> Cheers, >>> ed >>> >>> On 4 Feb 2014, at 14:27, Bruce Fischl wrote: >>> >>> Hi Ed, >>> >>> yes, although we reserve the values under 5 I >>> think for editing >>> changes, >>> I believe we only use 1 at the moment. >>> >>> cheers >>> Bruce >>> On Tue, 4 Feb 2014, Ed Gronenschild >>> wrote: >>> >>> Hi, >>> >>> From what I can read in the wiki >>> about wm editing, I understand >>> that edited wm voxels have values >>> of either 255 (added) or >>> 1 (removed) and no other values. >>> These are stored in the file >>> wm.mgz. Is that correct? >>> Before processing a lot of data I >>> want to be sure that running >>> recon-all with the option >>> autorecon2-wm will recognize these >>> voxels, also during longitudinal >>> processing. Can you confirm >>> this. >>> >>> FreeSurfer v5.3.0 Mac OSX10.6 >>> >>> Kind regards, >>> Ed >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> >>> 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 >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> --------------------------------- >>> Dr. Martin Reuter >>> Assistant in Neuroscience - Massachusetts General Hospital >>> Instructor in Neurology - Harvard Medical School >>> MGH / HMS / MIT >>> A.A.Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, MA 02129 >>> Phone: +1-617-724-5652 >>> Email: >>> [email protected] >>> [email protected] >>> Web : http://reuter.mit.edu >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
