Doug,
I want all GM.
Ed
On 26 Aug, 2009, at 18:53 , freesurfer-request@nmr.mgh.harvard.edu wrote:
For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want a particular GM or all GM?
Ed Gronenschild wrote:
Doug,
The file "segmentation.mgz" doesn't exist. I think that you mean that segmentation.mgz stands for either WM or GM. Can you provide me the exact file names of the final WM and GM segmentations.
Ed
On 25 Aug 2009, at 17:28, Douglas N Greve wrote:
mri_convert segmentation.mgz segmentation.nii
should do it
doug
Ed Gronenschild wrote:
Hi,
I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that?
Ed
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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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Hi Ed, sorry for the delay. For GM, you'll need to do the following:
1. Create a binary mask of the cortical GM: mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz This is just a thresholding operation. All the cortical areas have an index >= 1000.
2. Create a binary mask of the subcorical GM: mri_binarize --i aparc+aseg.mgz --o subctx.mgz --match 9 --match 10 --match 11 --match 12 --match 13 \ --match 18 --match 19 --match 26 --match 27 --match 28 --match 45 --match 48 ... This one is harder because you have to supply a match value for each subcortical gray matter structure. You can get these from $FREESURFER_HOME/FreeSurferColorLUT.txt
3. Add the cortical and subcortical: mri_concat subctx.mgz ctx.mgz --sum --o gm.mgz Note that you can make the output nifti instead (--o gm.nii)
doug
Ed Gronenschild wrote:
Doug,
I want all GM.
Ed
On 26 Aug, 2009, at 18:53 , freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
For WM, you can use aparc+aseg.mgz and use indices 2 and 41. Do you want a particular GM or all GM?
Ed Gronenschild wrote:
Doug,
The file "segmentation.mgz" doesn't exist. I think that you mean that segmentation.mgz stands for either WM or GM. Can you provide me the exact file names of the final WM and GM segmentations.
Ed
On 25 Aug 2009, at 17:28, Douglas N Greve wrote:
mri_convert segmentation.mgz segmentation.nii
should do it
doug
Ed Gronenschild wrote:
Hi,
I would like to extract the WM and GM segmentations used for the final cortical thickness calculations as nifti files. How can I do that?
Ed
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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Ed Gronenschild