Dear all, In an earlier post, I was asking for help implementing dilated ROIs.
I was using Doug's suggestion mri_aparc2aseg --subject 01 --a2009s --labelwm --wmparc-dmax 2 --o aparc.a2009s+aseg_liberal.mgz followed by mri_label2vol --seg aparc.a2009s+aseg_liberal.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 However, the written images are very similar to the original undilated ROIs, so I guess this has to do with the fact that they labels within white matter are still classified as white matter. My question: How can I write the ROIs from the dilated labels? Thanks! Martin P.S.: If this all is very difficult or impossible, I would be happy if I could just write out a nifti for each label in the annotation file which for each voxel reflects the probability of that label (i.e. not binary masks, but probabilistic masks). Then I could do this process manually. 2015-07-15 18:10 GMT+02:00 Martin Hebart <martin.heb...@gmail.com>: > Dear Thomas and Doug, > > Thanks a lot for your replies, I believe you fully answered my question. > > @Thomas: The reason I would like to dilate masks into white matter is that > although the masks are quite accurate for structural volumes, the > functional data doesn't perfectly fit the structural (even when using a > fieldmap). I don't want to miss any grey matter voxels that might carry > information, while including some white matter is - for the purpose of my > task - not detrimental. > > Thanks again, I will try to implement Doug's suggestion! > > Martin > > > > 2015-07-15 15:12 GMT+02:00 Thomas Yeo <ytho...@csail.mit.edu>: > >> Hi Martin, >> >> I am a little confused. Can you explain a little more about what you >> need? Do you want the freesurfer cortical ROIs dilated into the >> surrounding regions like white matter and CSF or something? If so, >> then Doug's suggestion sounds reasonable. >> >> In the case of my parcellation, I ran the MNI152 template through >> recon-all, which unfortunately resulted in an overly conservative >> estimate of gray matter (i.e., the tight mask in >> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). >> Therefore I went through a rather complicated way of generating the >> liberal mask by registering the recon-all of 1000 subjects to MNI >> space. >> >> Since you appear to be working on an individual subject, the >> freesurfer estimate of the cortical ROIs is likely to be quite >> accurate. Why might you want to dilate them into CSF or white matter? >> >> Regards, >> Thomas >> >> On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu> wrote: >> > There is not an easy way to do that, though Thomas might want to chime >> > in. I would probably use the code that generates the wmparc >> > (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a >> > few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels >> > >> > On 07/14/2015 08:18 AM, Martin Hebart wrote: >> >> Dear Freesurfer users, >> >> >> >> I would be really happy if someone could help me out on the issue I >> >> mentioned below. >> >> >> >> What I want to do is create non-overlapping anatomical ROI masks that >> >> are not restricted to grey matter only. >> >> >> >> Thanks a lot in advance! >> >> Martin >> >> >> >> --------- >> >> >> >> Dear all, >> >> >> >> I've created non-overlapping ROI masks using >> >> >> >> mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o >> >> rois.nii --temp sub.nii --subject 01 >> >> >> >> Now these ROI masks are actually quite conservative concerning grey >> >> matter vs. other structures, i.e. they are only on the grey matter. >> >> I've seen more liberal masks e.g. here: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 >> >> >> >> I would like to create similarly liberal non-overlapping ROI masks for >> >> all ROIs in the voxel size defined by the image in --temp, but >> >> excluding specific tissue types such as white matter, CSF, and other >> >> non-grey matter tissue. What would be the best way to do so? >> >> >> >> Cheers, >> >> Martin >> >> >> >> >> >> >> >> _______________________________________________ >> >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > >> > _______________________________________________ >> > 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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