It does not surprise me that it fails on the fsaverage surface. I agree with Marie that it is not good idea to use LGI on fsaverage for anything. Definitely not its intended purpose. doug
On 10/28/2014 03:06 PM, Marie Schaer wrote:
Hi Pierre,
I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks "cut". It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from.
But in any case, I wouldn't advice to run the LGI on the fsaverage, as the pattern of cortical folding is lost from the averaging of the subjects. So I'm not even sure that the algorithm will work even if you get mris_fill to work.
Can you tell us more precisely what you are trying to do? And why on the fsaverage rather than on your individual subject?
Best,
Marie
On Oct 28, 2014, at 5:31 AM, Pierre Mégevand <pierre.megevand@gmail.com mailto:pierre.megevand@gmail.com> wrote:
Dear all,
I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right.
It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen?
Thanks,
Pierre
Pierre Mégevand, MD, PhD PLOS Neuro Community http://neuro.plos.org/ editor - Follow us on Twitter http://twitter.com/PLOSNeuro Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter http://twitter.com/pierre_vanmedge- Read my blog here http://neuroscimed.wordpress.com/ <screenshot3.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer