Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha
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One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh, mgz, analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all, Does aseg save out masks of the various subcortical regions measured? If so, is it possible to visualize and/or edit these in tkmedit/scuba, or export them to an external format? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1
Doug Greve greve@nmr.mgh.harvard.edu 7/17/2006 7:14 pm >>>
One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh, mgz,
analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all, Does aseg save out masks of the various subcortical regions
measured?
If so, is it possible to visualize and/or edit these in
tkmedit/scuba,
or export them to an external format? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is relatively new. You can get it from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
doug
On Tue, 18 Jul 2006, Sasha Wolosin wrote:
Thanks! I don't have mri_binarize though. Is it included in 3.0.3? I am currently running stable 3.0.1
Doug Greve greve@nmr.mgh.harvard.edu 7/17/2006 7:14 pm >>>
One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh, mgz,
analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all, Does aseg save out masks of the various subcortical regions
measured?
If so, is it possible to visualize and/or edit these in
tkmedit/scuba,
or export them to an external format? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks. Regarding subcortical segmentation in general, if I am using a Philips scanner should I be using the flag -cross-sequence when calling mri_ca_label?
Doug Greve greve@nmr.mgh.harvard.edu 7/18/2006 10:54 am >>>
It is relatively new. You can get it from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
doug
On Tue, 18 Jul 2006, Sasha Wolosin wrote:
Thanks! I don't have mri_binarize though. Is it included in 3.0.3?
I
am currently running stable 3.0.1
Doug Greve greve@nmr.mgh.harvard.edu 7/17/2006 7:14 pm >>>
One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh,
mgz,
analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all, Does aseg save out masks of the various subcortical regions
measured?
If so, is it possible to visualize and/or edit these in
tkmedit/scuba,
or export them to an external format? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, you should use -align (which I think is the default now) On Tue, 18 Jul 2006, Sasha Wolosin wrote:
thanks. Regarding subcortical segmentation in general, if I am using a Philips scanner should I be using the flag -cross-sequence when calling mri_ca_label?
Doug Greve greve@nmr.mgh.harvard.edu 7/18/2006 10:54 am >>>
It is relatively new. You can get it from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
doug
On Tue, 18 Jul 2006, Sasha Wolosin wrote:
Thanks! I don't have mri_binarize though. Is it included in 3.0.3?
I
am currently running stable 3.0.1
Doug Greve greve@nmr.mgh.harvard.edu 7/17/2006 7:14 pm >>>
One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set them to 1 in the output. In this case, it will make a binary mask of the left cerebral white matter as that has a code of 2 (from FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh,
mgz,
analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all, Does aseg save out masks of the various subcortical regions
measured?
If so, is it possible to visualize and/or edit these in
tkmedit/scuba,
or export them to an external format? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If
you
are not the intended recipient, be advised that any unauthorized
use,
disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited.
If
you have received this e-mail in error, please immediately notify
the
sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Sasha Wolosin