I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks.
Chris On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > Hi Chris, I don't think there is such a tool. One thing you can do is to > use the aparc+aseg.mgz as the source instead of the lh and rh surfaces > separately. This might solve all of your problems. > doug > > > On 07/06/2012 12:02 PM, Christopher Bell wrote: > > > > Hello Freesurfers, > > > > > > I have developed a pipeline that uses mri_label2vol to take freesurfer > > parcellations to > > native fmri space, and uses dilation (within mri_label2vol) to make > > the ROIs larger since our resolution is only > > 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to > > large voxel > > size and partial voluming wihout the dilation. However, since the lh > > and rh are done > > separately by mri_label2vol, I now have overlap on the midline and > > have to go through a bunch > > of masking steps to eliminate it. > > > > My question is; is there a tool that will take both lh/rh > > parcellations to a new coordinate > > system, do dilation, and most importantly control for lh/rh overlap? > > Or any other > > similar suggestions. Thanks! > > > > Basically I am looking to rework my pipeline, and it seems I should be > > able > > to find a more parsimonious solution, than my "Rube Goldberg" approach. > > > > Chris > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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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