External Email - Use Caution
Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected but the visualization of the pial, white and inflated surfaces in freeview is somehow bad as you can see on the picture attached (lh.pial_freeview, lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and is there a way to correct it ? Or could it be a 3D rendering issue that can be fixed with visualization options ? Oddly, when I zoom really close for all surfaces, it seems perfectly smoothed... I thought first it could be linked to the topological defect correction (which I didn't do) but when I display the surfaces with paraview it works fine as you can also see on the picture attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). Everything works fine otherwise.
Thanks in advance for any help you may provide and I can send you some screenshots highlightening the issue or the recon-all log.
Best,
Achille Teillac
sorry, no picture attached. Can you resend?
On 11/29/2021 2:40 AM, achille.teillac@chu-lyon.fr wrote:
External Email - Use Caution
Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected but the visualization of the pial, white and inflated surfaces in freeview is somehow bad as you can see on the picture attached (lh.pial_freeview, lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and is there a way to correct it ? Or could it be a 3D rendering issue that can be fixed with visualization options ? Oddly, when I zoom really close for all surfaces, it seems perfectly smoothed... I thought first it could be linked to the topological defect correction (which I didn’t do) but when I display the surfaces with paraview it works fine as you can also see on the picture attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). Everything works fine otherwise.
Thanks in advance for any help you may provideand I can send you some screenshots highlightening the issue or the recon-all log.
Best,
Achille Teillac
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Achille
I don't think any attachments came through.
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of achille.teillac@chu-lyon.fr Sent: Monday, November 29, 2021 2:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Visualization error in freeview from recon-all
External Email - Use Caution Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected but the visualization of the pial, white and inflated surfaces in freeview is somehow bad as you can see on the picture attached (lh.pial_freeview, lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and is there a way to correct it ? Or could it be a 3D rendering issue that can be fixed with visualization options ? Oddly, when I zoom really close for all surfaces, it seems perfectly smoothed... I thought first it could be linked to the topological defect correction (which I didn't do) but when I display the surfaces with paraview it works fine as you can also see on the picture attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). Everything works fine otherwise.
Thanks in advance for any help you may provide and I can send you some screenshots highlightening the issue or the recon-all log.
Best,
Achille Teillac
freesurfer@nmr.mgh.harvard.edu
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achille.teillac＠chu-lyon.fr -
Douglas N. Greve -
Fischl, Bruce