thanks Dr. Fischl - it seems to match well so I will continue to use this method. It would be great if Ruopeng could eventually edit Freesurfer to allow for thresholding .labels too.
On another note, is there a way to edit labels in Freeview in a similar manner to doing so in tksurfer?* From what I can tell, one can only edit volume segmentations in Freeview.* best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Mon, Apr 25, 2016 at 8:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > yes, that sounds right. Does it look correct? That is, are areas 1/4 etc.. > in the central sulcus and such? > On Mon, 25 Apr 2016, Trisanna Sprung-Much wrote: > > Not a problem, Dr. Fischl! >> In the meantime, could you please confirm that I am opening up a >> cytoarchitectonic probability map I have as .mnc >> correctly? >> >> I basically change it to a surface overlay.mgz using mri_vol2surf and >> then open it as an overlay with a surface in >> Freeview. I can then change the thresholds using "configure overlay". >> >> best >> >> Trisanna >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Mon, Apr 25, 2016 at 6:53 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Trisanna >> >> yes, but Ruopeng is on vacation to it will be a while >> >> Bruce >> On Mon, 25 Apr 2016, Trisanna Sprung-Much wrote: >> >> Hi there >> >> With regards to this email from March, I cannot seem to be >> able to change >> thresholds of .labels in Freeview. Could this be added as an >> option? >> >> best wishes >> >> Trisanna >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> On Sun, Mar 13, 2016 at 1:45 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Trisanna >> >> 1. the .thresh labels have been thresholded with a >> p-value >> threshold that is "best" on our training set of >> manually/architectonically defined labels. >> >> 2. Hmmm, not sure, but we have stopped development on >> tksurfer. >> Can you try this on freeview? I can't remember if >> freeview >> allows changing thresholds in labels, but if not >> Ruopeng can add >> it to his list of feature requests >> >> cheers >> Bruce >> >> >> >> On Sat, 12 Mar 2016, Trisanna Sprung-Much wrote: >> >> Hi there >> I have two questions regarding using the labels >> with >> tksurfer: >> >> 1. What exactly has been done to change the .label >> (e.g. lh BA44.label) to >> .thresh.label (e.g. lh BA44.thresh.label? >> >> 2. The instructions on this page >> >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps >> >> to overlay the labels and set the Min and Max do >> not >> seem to work for me - I >> cannot seem to alter the Min from 2 and the Max >> from >> 5. Any thoughts as to >> why? >> >> thanks very much! >> >> Trisanna >> >> >> -- >> Ph.D. CandidateMcGill University >> Integrated Program in Neuroscience >> Psychology >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > _______________________________________________ > 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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