Thank you.
I just found this:
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
1) Is it better to extract the masks from the .mgz file (as explained on this
site) as opposed to converting the aparc+aseg-inhighres.mgz file to .nii.gz and
then extracting masks with FSL/AFNI?
2) Is there anyway to loop through all the labels instead of specifying by hand
in this command:
mri_label2vol –label ./lh.entorhinal.label –temp \
/Applications/freesurfer/subjects/${blindnum}/mri/rawavg.mgz –subject
${blindnum} –hemi lh –o \${blindnum}_lh_entorhinal.nii.gz –proj frac 0 1 .1
–fillthresh .3 –reg ../mri/register.dat
Thank you,
S
On 06/15/11, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
>
>
> You are guaranteed not to have overlap regardless of what you do as
> there is only one label at each voxel. For Cortex, what you have is
> fine. For subcortical, you can use what is in
> $FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
> which can be ignored.
>
> doug
>
> Sudhin A. Shah wrote:
> > Hi,
> >
> > Is there anyway to know all the label #s that are in
> > aparc+aseg-inhighres.mgz.
> >
> > Thank you,
> >
> > S
> >
> > On 06/13/11, *"Sudhin A. Shah" * <sut2...@med.cornell.edu> wrote:
> >> Hi Sorry for bothering you again, but I am not sure I understand.
> >>
> >> I was running whole brain correlation analysis (voxel by voxel). BUT
> >> for comparison purposes, I want to compute region by region
> >> correlation matrix.
> >> So, I want to divide up the brain into freesurfer parcellated regions
> >> - i.e. with no overlap, but with full coverage of whole brain.
> >>
> >> I have looked at FreeSurferColorLUT.txt and am confused because there
> >> are several sets and overlap (eg. 19 and 55 vs 2035..)
> >>
> >> If I use the following, can I ensure no overlap and full coverage?
> >> 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
> >> 2)Cortex: 1002- 1034, 2002- 2034
> >>
> >> I am asking if there is an established list of whole brain
> >> parcellations before I rely on label names to choose the ROIS
> >>
> >> On 06/13/11, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> wrote:
> >>> Anything that is non-0 will cover the whole brain.
> >>> doug
> >>>
> >>> Sudhin A. Shah wrote:
> >>> > Hi, thank you. Is there a range in the labels that will ensure
> >>> that I am including the whole brain? I.e. I see labels for Cx, but
> >>> not subcortical..
> >>> > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
> >>> >
> >>> > Thank you,
> >>> > S
> >>> >
> >>> >
> >>> >
> >>> > On Jun 13, 2011, at 10:59 AM, Douglas N Greve
> >>> <gr...@nmr.mgh.harvard.edu> wrote:
> >>> >
> >>> >
> >>> >> That is fine, or you can use mri_binarize with the --match
> >>> option. The numbers that correspond to each label can be found in
> >>> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them
> >>> visual as I described in my previous email with tkmedit:
> >>> >>
> >>> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg
> >>> >>
> >>> >> doug
> >>> >>
> >>> >>
> >>> >> Sudhin A. Shah wrote:
> >>> >>
> >>> >>> I mean that I am using FSL to create binary masks from
> >>> freesurfer parcellated regions. Unless there is a better way :)
> >>> >>>
> >>> >>> S
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve
> >>> <gr...@nmr.mgh.harvard.edu> wrote:
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>>> What do you mean you are doing it with FEAT?
> >>> >>>>
> >>> >>>> Sudhin A. Shah wrote:
> >>> >>>>
> >>> >>>>
> >>> >>>>> Hello,
> >>> >>>>>
> >>> >>>>> I am a beginner so please bear with me. I want to obtain
> >>> binary masks for every region (Cortical + subcortical). I am using
> >>> FSL(feat) to do this BUT am not sure what the labels would be.
> >>> >>>>>
> >>> >>>>> I have looked at FreeSurferColorLUT.txt for
> >>> aparc+aseg-in-highres.mgz BUT do not know which labels to use to
> >>> avoid overlap and ensure full coverage.
> >>> >>>>>
> >>> >>>>> Thank you,
> >>> >>>>>
> >>> >>>>> S
> >>> >>>>>
> >>> >>>>>
> >>> >>>>>
> >>> ------------------------------------------------------------------------
> >>> >>>>>
> >>> >>>>> _______________________________________________
> >>> >>>>> Freesurfer mailing list
> >>> >>>>> Freesurfer@nmr.mgh.harvard.edu
> >>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> >>>>> (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
> >>> >>>> (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
> >>> >>>> (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.
> >>> >>>>
> >>> >>>>
> >>> >>>>
> >>> >>>
> >>> >>>
> >>> >> --
> >>> >> 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
> >>> >>
> >>> >>
> >>> >
> >>> >
> >>> >
> >>>
> >>> --
> >>> 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
> >>> (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
> > (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
> (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
>
--
Sudhin A. Shah
Postdoctoral Fellow
Laboratory of Cognitive Neuromodulation
Weill Cornell Medical College, NY,NY
(212) 746-4514
_______________________________________________
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.
