Hi,
I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17)
Thank you for your consideration.
Best wishes,
Hi Salil, You should be able to apply an isosurface to each subfield label in freeview. You can set the color for each isosurface as well, since the default is gray. You need to be in the 3D view in order to display isosurfaces. -Louis
On Thu, 6 Feb 2014, Salil Soman wrote:
Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17)
Thank you for your consideration.
Best wishes,
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
Thank you for your email. I have been using the command:
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
to visualize the hippocampal subfield segmentations. However this created the posterior_ entries, which when I turn on the isosurface view, makes a solid structure, which I can adjust the color. But when I try to load in the individual volumes (e.g. posterior_right_CA2_3.mgz) I get a separate structure that is not at all registered with the right hippocampus. Any suggestions on what I am doing incorrectly?
-S
On Thu, Feb 6, 2014 at 10:38 AM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
Hi Salil, You should be able to apply an isosurface to each subfield label in freeview. You can set the color for each isosurface as well, since the default is gray. You need to be in the 3D view in order to display isosurfaces. -Louis
On Thu, 6 Feb 2014, Salil Soman wrote:
Hi,
I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17)
Thank you for your consideration.
Best wishes,
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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You can use the isosurface approach for a fast visualization. With a little more work you can generate a surface from your data and get a result like the attached picture. Em Qui, 2014-02-06 às 01:04 -0800, Salil Soman escreveu:
Hi,
I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17)
Thank you for your consideration.
Best wishes,
-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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Louis Nicholas Vinke -
Marcos Martins da Silva -
Salil Soman