Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
To go back to the original space, you can
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-source.mgz --interp nearest --regheader
doug
Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ 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
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think Doug answered that, didn't he?
On Tue, 2 Jan 2007, Kai Li wrote:
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tried replace --mov with --in, it complained that --tar is unknown. I actually couldn't find the options --mov, --tar, --o, and --regheader in the mri_vol2vol help. Is this because I'm using an older or newer version of freesurfer?
Thanks Kai
To go back to the original space, you can
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-source.mgz --interp nearest --regheader
doug
On Tue, 2 Jan 2007, Bruce Fischl wrote:
I think Doug answered that, didn't he?
On Tue, 2 Jan 2007, Kai Li wrote:
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ 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
I think you have an older version. Try the one in:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
Kai Li wrote:
Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tried replace --mov with --in, it complained that --tar is unknown. I actually couldn't find the options --mov, --tar, --o, and --regheader in the mri_vol2vol help. Is this because I'm using an older or newer version of freesurfer?
Thanks Kai
To go back to the original space, you can
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-source.mgz --interp nearest --regheader
doug
On Tue, 2 Jan 2007, Bruce Fischl wrote:
I think Doug answered that, didn't he?
On Tue, 2 Jan 2007, Kai Li wrote:
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ 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
Hi Doug, Is the executable you provided below a rh9 build? It seems that it isn't. It reported an error indicating it might be a build for something else. Could you please send a rh9 build?
/mri_vol2vol: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
Thanks, Kai On Wed, 3 Jan 2007, Doug Greve wrote:
I think you have an older version. Try the one in:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
Kai Li wrote:
Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tried replace --mov with --in, it complained that --tar is unknown. I actually couldn't find the options --mov, --tar, --o, and --regheader in the mri_vol2vol help. Is this because I'm using an older or newer version of freesurfer?
Thanks Kai
To go back to the original space, you can
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-source.mgz --interp nearest --regheader
doug
On Tue, 2 Jan 2007, Bruce Fischl wrote:
I think Doug answered that, didn't he?
On Tue, 2 Jan 2007, Kai Li wrote:
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to?
Thanks, Kai _______________________________________________ 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
-- 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
I'm sure it was a centos build. Nick, do we have an rh9 build that we get a copy of mri_vol2vol to give to Kai?
Kai Li wrote:
Hi Doug, Is the executable you provided below a rh9 build? It seems that it isn't. It reported an error indicating it might be a build for something else. Could you please send a rh9 build?
/mri_vol2vol: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
Thanks, Kai On Wed, 3 Jan 2007, Doug Greve wrote:
I think you have an older version. Try the one in:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
Kai Li wrote:
Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tried replace --mov with --in, it complained that --tar is unknown. I actually couldn't find the options --mov, --tar, --o, and --regheader in the mri_vol2vol help. Is this because I'm using an older or newer version of freesurfer?
Thanks Kai
To go back to the original space, you can
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-source.mgz --interp nearest --regheader
doug
On Tue, 2 Jan 2007, Bruce Fischl wrote:
I think Doug answered that, didn't he?
On Tue, 2 Jan 2007, Kai Li wrote:
Hi Bruce, Thanks a lot for your response. Still another question: it seems that ribbon.mgz is in the space of 1x1x1mm, isn't it? If that is the true, I wonder how to transform it back to the original input space.
Thanks, Kai
On Tue, 2 Jan 2007, Bruce Fischl wrote:
Hi Kai,
I think you can use the ribbon.mgz for cortical gray matter, and they aseg for other things.
cheers, Bruce On Tue, 2 Jan 2007, Kai Li wrote:
> Hi, > I wonder how to get masks on the cerebral white matter and the > cerebral cortex. In particular, I'd like to have the masks in > the space of the original input image. I noticed that in the > asegm.mgz cerebral white matter and cerebral cotex are > explicitly labeled, but I'm not sure if this is the final result > instead of an intermediate result of less accuracy. If I should > use aseg.mgz, do I need to do some transformation to go back to > the original space, and how to? > > Thanks, > Kai > _______________________________________________ > 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
-- 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Kai Li