Hi Mads
my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage
cheers Bruce
On Mon, 5 Oct 2015, Mads Jensen wrote:
Hi,
I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually.
The sequence is a MP2RAGE recorded from a Siemens Skyra.
thanks, mads
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jp... https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jp... https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jp... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer