Hi Bruce, Thanks for your help yesterday. I was able to create the .mgh file using the -output_type mgh option, but I am still unable to load it in tksurfer as label or anything else. If you or Doug have any other suggestions, I would really appreciate it. Thanks!
Jonathan On Sun, May 12, 2013 at 4:55 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Jonathan > > try -output_type mgh. It should create a "volume" that is nvertices long. > Not sure if it can directly create a label file, maybe Doug knows? > > > Bruce > > > On Sun, 12 May 2013, Jonathan DuBois wrote: > > I used the following options: mri_vol2surf --hemi lh --regheader subject01 >> --cortex --mov label.mgz --o ./label.mghIt ran without error, but I could >> >> not open the resulting file in tksurfer as either a label or an overlay: >> --------- >> /Applications/freesurfer/**tktools/tksurfer.bin: no data in label file >> /Users/label.mgh >> tkmedit: Trying to open /Users/label.dat >> surfer: Interpreting overlay volume /Users/label.mgh as encoded scalar >> volume >> >> Best, >> Jonathan >> >> >> On Sun, May 12, 2013 at 1:57 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> try using --regheader >> >> cheers >> Bruce >> On Sun, 12 May 2013, Jonathan DuBois wrote: >> >> Hi Bruce, >> I would like to convert the .mgz label volume to a >> surface label for that >> subject, but mri_vol2surf requires a registration >> file. >> >> Best, >> Jonathan >> >> >> >> On Sunday, May 12, 2013, Bruce Fischl wrote: >> Hi Jonathan >> >> you don't need to register it if it's shown >> properly in tkmedit >> or freeview. Can you tell us more about what >> you are trying to >> do? >> Bruce >> >> >> On Sun, 12 May 2013, Jonathan DuBois wrote: >> >> Hi Bruce, >> Thanks for the quick response. The label >> is a >> manually traced area of the >> cortex. It is in subject scanner space >> and has a >> single value, so it >> probably would not work with bbregister. >> I can load >> it in tkmedit as a >> segmentation and the alignment is >> correct. I >> attached a screenshot. Is there >> a way to select the values greater than >> zero in >> tkmedit and save as a label >> that could be used in vol2surf? I have >> other labels >> that are larger so I >> would prefer not to retrace them if >> possible. >> >> Inline image 2 >> Best, >> Jonathan >> >> >> On Sun, May 12, 2013 at 10:11 AM, Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Jonathan >> >> what is the label? What space is >> it in? If it >> has gray/white >> contrast you could try bbregister. >> >> cheers >> Bruce >> On Sat, 11 May 2013, Jonathan >> DuBois wrote: >> >> Hi Freesurfer Experts, >> I have a binary volume label >> in subject >> space that I >> converted from MINC to MGZ. >> I would like >> to register >> it to >> the surface of that subject >> as a flat >> label. I >> thought I would be able to >> do so with >> mri_vol2surf >> but I am not >> sure how to generate the >> required >> registration file. >> Is that the correct command, >> and if so, >> which >> registration >> file should I use? >> >> Thanks >> Jonathan >> >> >> >> >> 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. >> >> >> >> >> >> >>
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