Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin
we don't actually have a way to edit the pial surface. Usually, the problem you describe is an intensity normalization problem, so you might want to put some control points near the place where the pial surface is in error. Be careful putting in the control points. You want to make sure that they are truly in white matter. Look at the control points/intensity normalization tutorial on the wiki.
doug
?? wrote:
Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug, Thank you for your suggestion, We tried to add some control point and recreate the final surfaces according to the control points tutorial on the wiki as you suggested. Some regions looked better than before, however, there are still some regions which were still not included in the pial surface , that is, the red line dose not include some grey matter volume, like showed in the attachment, indicated by the yellow arrow. So, in this situation, is there any way to edit the pial and make the volumes in the red line finally? As the tutorial told how to delete pial in FsTutorial/PialEditshttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits, and we just want to do the opposite thing. Too much thanks! Jin
2010/8/24 Douglas N Greve greve@nmr.mgh.harvard.edu
we don't actually have a way to edit the pial surface. Usually, the problem you describe is an intensity normalization problem, so you might want to put some control points near the place where the pial surface is in error. Be careful putting in the control points. You want to make sure that they are truly in white matter. Look at the control points/intensity normalization tutorial on the wiki.
doug
?? wrote:
Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditshas showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
That spot looks to be in hippocampus in which case the surface is undefined (so don't try to fix it!). Don't worry about the surfaces that go through the midline or subcortical structures.
doug
?? wrote:
Dear Doug, Thank you for your suggestion, We tried to add some control point and recreate the final surfaces according to the control points tutorial on the wiki as you suggested. Some regions looked better than before, however, there are still some regions which were still not included in the pial surface , that is, the red line dose not include some grey matter volume, like showed in the attachment, indicated by the yellow arrow. So, in this situation, is there any way to edit the pial and make the volumes in the red line finally? As the tutorial told how to delete pial in FsTutorial/PialEdits https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits, and we just want to do the opposite thing. Too much thanks! Jin
2010/8/24 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
we don't actually have a way to edit the pial surface. Usually, the problem you describe is an intensity normalization problem, so you might want to put some control points near the place where the pial surface is in error. Be careful putting in the control points. You want to make sure that they are truly in white matter. Look at the control points/intensity normalization tutorial on the wiki. doug ?? wrote: Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin ------------------------------------------------------------------------ _______________________________________________ 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Hi Jin
you have to identify the problem. Is it that the white matter surface is incorrect so the pial doesn't get out far enough? Are the intensites in the wm and gm darker in that region? Is there a gm leson? If you upload the dataset we'll take a look
cheers Bruce
On Tue, 24 Aug 2010, [GB2312] Àîèª wrote:
Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
李瑾