[Freesurfer] make_average_subject error: could not load norm volume from (null)

External Email - Use Caution HI FreeSurfer Developers, I'm attempting to create an average subject make_average_subject but I get the error message the following error when I run the make_average_command: Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz ASeg

Re: [Freesurfer] recon-all error on ubuntu 16.04

"sudo apt-get" tools to install a pre 5.22 version of perl on > your machine. > > Hope this helps. > > -Zeke > > > > > > On 05/11/2016 10:06 AM, Mads Jensen wrote: >> Hi Martin, >> >> Thanks for your reply. >> >> rawavg.mgz and

Re: [Freesurfer] recon-all error on ubuntu 16.04

orrect.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > directly? Maybe something is wrong with the MNI tools. > > Best, Martin > > On 05/11/2016 07:43 AM, Mads Jensen wrote: >> Dear FreeSurfer group, >> >> I get

[Freesurfer] recon-all error on ubuntu 16.04

Dear FreeSurfer group, I get an error trying to run basic recon-all on a ubuntu 16.04 system. It finish with errors after a few minutes and I cannot find any help in the recon-all.log (pasted below). I have made the symbolic links from the installation notes. Any ideas or thoughts on what the

Re: [Freesurfer] Problem with recon-all

could be wrong. I'll cc Andre van der Kouwe who will know >> >> >> On Mon, 5 Oct 2015, Mads Jensen wrote: >> >>> Hi and thanks for the fast reply. >>> >>> Pardon my ignorance, but I am not sure that the PD images are? >>> >>> th

Re: [Freesurfer] Problem with recon-all

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, >&g

[Freesurfer] Problem with recon-all

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

Re: [Freesurfer] brainmask error

of the midline are notoriously bad for judging skull stripping accuracy cheers Bruce On Tue, 19 Aug 2014, Mads Jensen wrote: Dear list, I have problem with the brainmask from a subject where there is removed to much of the gray matter. So, I would like to hear if someone has a good idea where I should