You'll need to merge the WM parcellation labels with those of their
matching GM parcellations. We do not have explicit software to do this.
You can do it in matlab, something like
a = MRIread('aparc.a2009s+aseg_liberal.mgz");
ind = find(a.vol == 3030); % 3030 = wm-lh-superiortemporal from
FreeSurferColorLUT.txt
a.vol(ind) = 1030; % 1030 = ctx-lh-superiortemporal
Do the rest of the parcellations in the same way, then
MRIwrite(a,'aparc.a2009s+aseg_liberal2.mgz');
On 08/10/2015 01:29 PM, Martin Hebart wrote:
> 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
> <mailto: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
> <mailto: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 <mailto: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
> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://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
> <mailto: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
--
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
