Hi Bruce and Doug, thanks for looking into this and sorry for the delay. The command line we are using is:
mri_label2label --srclabel /Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p8.label --srcsubject y$1 --trglabel /Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp2.label --trgsubject yx$1 --regmethod surface --hemi lh We have several anatomies from the same subject, acquired on different occasions. We defined labels based on results of an fMRI experiment, and tried to use mri_label2label to map them within subjects from one anatomy to another. As a control, we also wanted to map the Hinds V1 from one anatomy to another, but this is where we ran into these holes. We will make an example subject available for debugging later today. Thanks! Caspar 2015-07-24 12:33 GMT-04:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > what is your command line? What do you mean by one anatomy to another? > > > On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: > > > > ---------- Forwarded message ---------- > From: *Caspar M. Schwiedrzik* <cschwie...@rockefeller.edu> > Date: Thursday, July 16, 2015 > Subject: problem with mri_label2label - large amount of holes > To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > > > Hi! > We are doing some analyses in which we map custom labels from one anatomy > to another, within subjects. As a control, we also tried to map > anatomically defined V1s according to the method by Hinds within subject > from one anatomy to another. However, as you can see in the attachment, > there are very many holes in the labels after using mri_label2label. This > does not happen with smaller labels. Why is this happening and is there a > solution? > Thanks, Caspar > > > > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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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