I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
Hi Derin,
it's pretty much impossible to tell if surfaces are crossing from a 2d slice. This looks like there was an incorrectly fixed topological defect in the hippocampus. You could manually correct it in the wm.mgz volume, but we don't really care about the surfaces in this region (cerebral cortex)
cheers, Bruce On Wed, 31 Jan 2007, Derin Cobia wrote:
I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
Bruce,
Are the things I'm noticing due to using 3.0.3 for everything (including topology fixer) up to final surfaces, then using 3.0.4? So I guess the other "odd" surfaces are acceptable to trust (excluding the medial temp lobe)?
Thanks!
Derin
Hi Derin,
it's pretty much impossible to tell if surfaces are crossing from a 2d slice. This looks like there was an incorrectly fixed topological defect in the hippocampus. You could manually correct it in the wm.mgz volume, but we don't really care about the surfaces in this region (cerebral cortex)
cheers, Bruce On Wed, 31 Jan 2007, Derin Cobia wrote:
I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
not really sure. Does the aseg look good? We don't usually see that kind of defect. On Wed, 31 Jan 2007, Derin Cobia wrote:
Bruce,
Are the things I'm noticing due to using 3.0.3 for everything (including topology fixer) up to final surfaces, then using 3.0.4? So I guess the other "odd" surfaces are acceptable to trust (excluding the medial temp lobe)?
Thanks!
Derin
Hi Derin,
it's pretty much impossible to tell if surfaces are crossing from a 2d slice. This looks like there was an incorrectly fixed topological defect in the hippocampus. You could manually correct it in the wm.mgz volume, but we don't really care about the surfaces in this region (cerebral cortex)
cheers, Bruce On Wed, 31 Jan 2007, Derin Cobia wrote:
I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
Aseg looks good, here's another example of what I'm finding. It's posterior midline (~PreCuneus area). Sometimes this happens on the outer cortical surfaces too. Thanks.
-Derin
not really sure. Does the aseg look good? We don't usually see that kind of defect. On Wed, 31 Jan 2007, Derin Cobia wrote:
Bruce,
Are the things I'm noticing due to using 3.0.3 for everything (including topology fixer) up to final surfaces, then using 3.0.4? So I guess the other "odd" surfaces are acceptable to trust (excluding the medial temp lobe)?
Thanks!
Derin
Hi Derin,
it's pretty much impossible to tell if surfaces are crossing from a 2d slice. This looks like there was an incorrectly fixed topological defect in the hippocampus. You could manually correct it in the wm.mgz volume, but we don't really care about the surfaces in this region (cerebral cortex)
cheers, Bruce On Wed, 31 Jan 2007, Derin Cobia wrote:
I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
Try looking at it in a different view. Sometimes the surface is almost parallel to the viewing plane in which case it crosses it many times in a short span.
On Wed, 31 Jan 2007, Derin Cobia wrote:
Aseg looks good, here's another example of what I'm finding. It's posterior midline (~PreCuneus area). Sometimes this happens on the outer cortical surfaces too. Thanks.
-Derin
not really sure. Does the aseg look good? We don't usually see that kind of defect. On Wed, 31 Jan 2007, Derin Cobia wrote:
Bruce,
Are the things I'm noticing due to using 3.0.3 for everything (including topology fixer) up to final surfaces, then using 3.0.4? So I guess the other "odd" surfaces are acceptable to trust (excluding the medial temp lobe)?
Thanks!
Derin
Hi Derin,
it's pretty much impossible to tell if surfaces are crossing from a 2d slice. This looks like there was an incorrectly fixed topological defect in the hippocampus. You could manually correct it in the wm.mgz volume, but we don't really care about the surfaces in this region (cerebral cortex)
cheers, Bruce On Wed, 31 Jan 2007, Derin Cobia wrote:
I reran our subjects from "final_surfaces" on through autorecon3 using 3.0.4 to correct for the pial surface crossover at the midline (as recommended by Bruce). Most things look fine, except that there are many portions of the surfaces that appear to "bunch" together. In one extreme example it appears that the white and pial surface cross. I've attached some jpgs to demonstrate what I mean. The close-up is r medial temporal area, while the other shows the "bunching" in the l superior portion, and at the midline. I understand that the crossing is not correct, but do the other surfaces look appropriate? Thanks.
-Derin
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Derin Cobia