Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring.
One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this?
Many thanks for any feedback you can provide.
Jason
Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring.
One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this?
Many thanks for any feedback you can provide.
Jason
I've done a little of this kind of thing, mostly tracking from thalamus or amygdala to cortex, not starting at cortex, but the problem would be the same. I have not had the problem that you describe, even when starting at voxels clearly interior to thalamus (none of which is actually labeled as white matter in the segmentation). Do you think this would generalize to your concern?
The way that we usually do the mapping into the diffusion space is to map the aparc+aseg.mgz rather then the surfaces themselves. This could help or hurt the partial voluming.
doug
Jason Tourville wrote:
Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring.
One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this?
Many thanks for any feedback you can provide.
Jason
-- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Cognitive and Neural Systems Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
FSL's tools don't use an FA threshold for tractography. So long as there is a consistent direction(s) to follow it will track through a voxel.
Peace,
Matt.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, November 10, 2010 4:26 PM To: Jason Tourville Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer ROI masks for DTI tractograpy
I've done a little of this kind of thing, mostly tracking from thalamus or amygdala to cortex, not starting at cortex, but the problem would be the same. I have not had the problem that you describe, even when starting at voxels clearly interior to thalamus (none of which is actually labeled as white matter in the segmentation). Do you think this would generalize to your concern?
The way that we usually do the mapping into the diffusion space is to map the aparc+aseg.mgz rather then the surfaces themselves. This could help or hurt the partial voluming.
doug
Jason Tourville wrote:
Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring.
One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this?
Many thanks for any feedback you can provide.
Jason
-- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Cognitive and Neural Systems Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755
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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Douglas N Greve -
Jason Tourville -
Matt Glasser