Re: [Freesurfer] Cortical labels for WM seeding
Hi Sean I think using mris_expand with a negative number is the better way to do this. Then use the resulting surface for the seed. It should prevent the surface from passing through itself (which is what you are seeing) cheers Bruce On Mon, 9 Sep 2013, Sean Hatton wrote: > Hello FS Gurus, > > I would like to export FS labels as seed regions for deterministic > tractography in TrackVis (probabilistic is not appropriate in this > investigation). I run mri_label2vol with ?--proj abs -4 0 .1? to try and grow > the label into the WM and exclude GM. While I get a biologically plausible > ROIs and plenty of good streamlines, I do get some stray streamlines that > jump across the sulci into adjacent gyri which (I have read) is an artefact > of seeding from GM. Have I got the right approach? Should I create an inverse > intracranial volume mask as an exclusion mask? Something else? > > Kind regards, > > Sean Hatton > Brain & Mind Research Institute > University of Sydney, Australia. > ___ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical labels for WM seeding
I'd probably try GM plus a (DWI-sized) voxel or so into the WM. On Mon, 9 Sep 2013, Sean Hatton wrote: Great, I will give that a shot. In the seeding ROI should I combine the gm and wm labels or is the GM sufficient to encapsulate, say, the superior temporal gurus GM and WM? Anastasia Yendiki wrote: Hi Sean - Do you mean that the streamlines go through non-brain voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain & Mind Research Institute University of Sydney, Australia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical labels for WM seeding
Great, I will give that a shot. In the seeding ROI should I combine the gm and wm labels or is the GM sufficient to encapsulate, say, the superior temporal gurus GM and WM? Anastasia Yendiki wrote: Hi Sean - Do you mean that the streamlines go through non-brain voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: > Hello FS Gurus, > > I would like to export FS labels as seed regions for deterministic > tractography in TrackVis (probabilistic is not appropriate in this > investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and > grow the label into the WM and exclude GM. While I get a biologically > plausible ROIs and plenty of good streamlines, I do get some stray > streamlines that jump across the sulci into adjacent gyri which (I have > read) is an artefact of seeding from GM. Have I got the right approach? > Should I create an inverse intracranial volume mask as an exclusion > mask? Something else? > > Kind regards, > > Sean Hatton > Brain & Mind Research Institute > University of Sydney, Australia. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical labels for WM seeding
Hi Sean - Do you mean that the streamlines go through non-brain voxels? You could you a slightly dilated version of the aparc+aseg as a mask. You can use bbregister to map it to the subject's DWI space. a.y On Mon, 9 Sep 2013, Sean Hatton wrote: Hello FS Gurus, I would like to export FS labels as seed regions for deterministic tractography in TrackVis (probabilistic is not appropriate in this investigation). I run mri_label2vol with “--proj abs -4 0 .1” to try and grow the label into the WM and exclude GM. While I get a biologically plausible ROIs and plenty of good streamlines, I do get some stray streamlines that jump across the sulci into adjacent gyri which (I have read) is an artefact of seeding from GM. Have I got the right approach? Should I create an inverse intracranial volume mask as an exclusion mask? Something else? Kind regards, Sean Hatton Brain & Mind Research Institute University of Sydney, Australia. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
RE: [Freesurfer] cortical labels
recon-all already creates such a volume. Look at aparc+aseg.mgz. You can load it as a segmentation, same as aseg.mgz On Wed, 15 Mar 2006, Kevin Teich wrote: but I would still like to know if there is anyway to build an mgz image of the grey volume segmented accordingly to ?h.aparc.annot. I hope you can help me. In tksurfer, you can import an annotation as a segmentation file. This will fill the voxels between surfaces with the label in the annotation file. Then you can save this segmentation as a new volume. -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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
RE: [Freesurfer] cortical labels
> but I would still like to know if there is anyway to build an mgz > image of the grey volume segmented accordingly to ?h.aparc.annot. I > hope you can help me. In tksurfer, you can import an annotation as a segmentation file. This will fill the voxels between surfaces with the label in the annotation file. Then you can save this segmentation as a new volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] cortical labels
thank you very much Bruce, but I would still like to know if there is anyway to build an mgz image of the grey volume segmented accordingly to ?h.aparc.annot. I hope you can help me. thanks, -ste -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 3/14/2006 2:58 PM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical labels the ?h.aparc.annot file contains this info, but as a surface file. Load it in tksurfer via file->label->import annotation. cheers, Bruce On Tue, 14 Mar 2006, Pellegrini, Stefano (NIH/NINDS) [F] wrote: > > Hi everybody, > > I have seen that the aseg.mgz file allows to see the segmentation of the > whole brain volume in different areas. Is there any way to obtain an mgz file > with the cortical gray matter volume labeled in such a way that every > cortical region has a different intensity value? > thanks, > >-stefano > > ___ > 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
Re: [Freesurfer] cortical labels
the ?h.aparc.annot file contains this info, but as a surface file. Load it in tksurfer via file->label->import annotation. cheers, Bruce On Tue, 14 Mar 2006, Pellegrini, Stefano (NIH/NINDS) [F] wrote: Hi everybody, I have seen that the aseg.mgz file allows to see the segmentation of the whole brain volume in different areas. Is there any way to obtain an mgz file with the cortical gray matter volume labeled in such a way that every cortical region has a different intensity value? thanks, -stefano ___ 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
