Thank you.
I just found this: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-fr...
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 greve@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" * sut2006@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 * greve@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
greve@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
greve@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 >>> >>> >>>
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Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 greve@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
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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