I used the following options: mri_vol2surf --hemi lh --regheader subject01 --cortex --mov label.mgz --o ./label.mgh It 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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