Hi Martin
at the end of recon-all we correct the volume-based segmentations with
the surfaces, so the aparc*.mgz files should be pretty accurate
cheers
Bruce
On Thu, 2
Jul 2015, Martin Hebart wrote:
Hi Doug,
Thanks a lot. But aren't the aparc.a2009s+aseg.mgz the volume-based ROIs and
aren't they less accurate than the surface-based ones?
Best,
Martin
Am 02.07.2015 14:47 schrieb "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>:
I would just use the 2nd command since aparc.a2009s+aseg.mgz
will have
already resolved the issues of overlap that you mention.
doug
On 07/02/2015 04:07 AM, Martin Hebart wrote:
> Here's the exact code that I used:
>
> surface:
> mri_label2vol --annot aparc.a2009s.annot --regheader
> $1/$2/mri/orig.mgz --o $1/$2/roi/mask_lh.nii --temp
$1/$2/mri/orig.mgz
> --subject $2 --hemi lh --proj frac 0 1 .1
>
> same for the right hemisphere.
>
> volumetric:
> mri_label2vol --seg $1/$2/mri/aparc.a2009s+aseg.mgz
--regheader
> $1/$2/mri/orig.mgz --o $1/$2/roi/mask_vol.nii --temp
> $1/$2/mri/orig.mgz --subject $2
>
> Cheers,
> Martin
>
>
> 2015-07-01 23:38 GMT+02:00 Douglas N Greve
<gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>:
>
> How did you create the ROIs?
>
> On 07/01/2015 12:25 PM, Martin Hebart wrote:
> > Dear members of the list,
> >
> > I'm new to Freesurfer, so please excuse me asking
possibly basic
> > questions. I have spent quite some time on the wiki and
searching
> > through the emails before writing to the list, but I
might have
> missed
> > some important information.
> >
> > I would like to work on anatomical ROIs created based on
> Freesurfer's
> > surface-based and volumetric ROIs and continue working
with them in
> > nifti format (e.g. for SPM). If I understand it
correctly, the
> > surface-based ROIs should take into account the
individual subject's
> > anatomy better than the volumetric ROIs would. At the
same time, for
> > subcortical regions it is necessary to use volumetric
ROIs.
> >
> > I did recon -all, followed by extracting all surface
ROIs using
> > mri_label2vol --annot aparc.a2009s.annot and the
volumetric ROIs
> using
> > mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I
manually
> > removed all cortical labels from the volumetric ROIs.
> >
> > Now when looking at the ROIs, they overlap slightly,
both
> between left
> > and right hemisphere (roughly 150 voxels), and between
the
> hemispheres
> > and the subcortical regions (roughly 300 voxels).
> >
> > Is there a way I can assign the masks volumes a unique
label? I was
> > considering removing these voxels, but ideally I would
just keep
> them
> > in and use the label with the highest probability. Or is
there an
> > alternative suggestion that makes more sense (e.g.
rather
> attributing
> > overlapping regions to subcortical regions)?
> >
> > Thanks a lot in advance for your reply!
> > 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
_______________________________________________
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.
