[Freesurfer] LGI and its relationship with other metrics.

2017-09-08 Thread Caverzasi, Eduardo
Dear Freesurfer expert, I am writing regarding the local gyrification index (lGI), pipeline now available with Freesurfer. In order to better understand the results obtained it would be important to better understand the relationship between lGI to other metrics provided by the freesurfer ana

Re: [Freesurfer] Transfer files from Windows

2017-09-08 Thread Kanoff, Kristen Elise
Are you running a Linux VirtualBox on a Windows desktop? If so, you should ignore the step that mentions the VBOXSRV directory (that is only relevant if you are running a Windows VirtualBox on a Linux/Mac desktop). If you followed all the instructions in the link provided in the prior response

Re: [Freesurfer] Transfer files from Windows

2017-09-08 Thread Fereshte
I've tried this before but i couldn't find VBOXSRV in the mentioned directory. On Fri, Sep 8, 2017 at 10:31 PM Patrycja Naumczyk < patrycja.naumc...@gmail.com> wrote: > It is widely described on the Internet. Try searching for "Virtual Box > share files", i.e.: > > https://www.howtogeek.com/189974

Re: [Freesurfer] Transfer files from Windows

2017-09-08 Thread Patrycja Naumczyk
It is widely described on the Internet. Try searching for "Virtual Box share files", i.e.: https://www.howtogeek.com/189974/how-to-share-your-computers-files-with-a-virtual-machine/ 2017-09-08 18:07 GMT+02:00 Fereshte : > Dear FreeSurfer experts > I've tried using FreeSurfer on windows with Virtu

[Freesurfer] Transfer files from Windows

2017-09-08 Thread Fereshte
Dear FreeSurfer experts I've tried using FreeSurfer on windows with VirtualBox. I need to transfer some files on my windows to use in FreeSurfer. I've seen the same question in the frum but not appropriate answer and i couldn't find any helpful instructions on net either. I'd appreciate your help w

Re: [Freesurfer] PETsurf non linear registration

2017-09-08 Thread Douglas Greve
The method used to correct for the volume fraction effect is detailed in our paper: Greve, Douglas N., et al. "Different partial volume correction methods lead to different conclusions: An 18 F-FDG-PET study of aging." /Neuroimage/ 132 (2016): 334-343. There is not a way to include a non-lin

[Freesurfer] PETsurf non linear registration

2017-09-08 Thread Victor Montal Blancafort
Dear Freesurfer experts, I have been working with the PETsurf pipeline. I was wondering if there is any chance to use a non-linear registration (i.e ANTS) in order to compute the %tissue per voxel in native space. Currently, I am using your pipeline to process DWI data. Due to some EPI artifacts

Re: [Freesurfer] LME model and contrast

2017-09-08 Thread Diers, Kersten /DZNE
Seems fine to me. As a side-note, you may want to consider centering bslBMI and other continuous predictors (other than time), and time should be time_from_baseline. Best, Kersten From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mg

Re: [Freesurfer] patch for ribbon mgz failure. SAME ERROR

2017-09-08 Thread Maria Gloria Rossetti
Yes it does. I ran -cortribbon first then reran autorecon-all (instead of -autorecon2). Now it finished "without error". However I'm still confused why do I get the error when I run -autorecon2 (a freesurfer newbie over here) Best, Gloria Da: "Douglas Greve" A: "freesurfer" Inviato: Mer

Re: [Freesurfer] longitudinal freesurfer- different scanners

2017-09-08 Thread Martin Reuter
Hi Michelle, when scanners (or even scanner hardware, like head coil or software upgrades etc) change in a longitudinal study you will have difficulties finding out whether the changes you see are real anatomical changes or scanner effects. This is true for any software pipeline (longitudinal