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.
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
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 ayendiki@nmr.mgh.harvard.edu 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.
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 ayendiki@nmr.mgh.harvard.edu 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.
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@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Bruce Fischl -
Sean Hatton