Re: [Freesurfer] Calcarine fissure is divided into parts in the flat map

2009-01-26 Thread Bruce Fischl
it's because of the cut. cheers, Bruce On Mon, 26 Jan 2009, Jürgen Hänggi wrote: Dear FS experts The calcarine fissure (shown in cyan) is divided into several parts in the flat map. All other areas are still in one part in the flat map (see attachment). Is there anything wrong or is this the

Re: [Freesurfer] Freesurfer 4.0.5 Leopard

2009-01-26 Thread Nick Schmansky
Ming, Do you have the latest Apple updates? The latest is up to 10.5.6. They fixed a lot of stuff related to X11. Nick On Sat, 2009-01-24 at 22:04 -0600, Ming Hsu wrote: Hi Nick, I was able to download 4.0.5, and everything runs fine on the desktop. However over ssh, qdec seems to

Re: [Freesurfer] Freesurfer 4.0.5 Leopard

2009-01-26 Thread Nick Schmansky
Ming, Also you can try using the -Y or -X flag with ssh, which enables X11 forwarding. Nick On Mon, 2009-01-26 at 11:27 -0500, Nick Schmansky wrote: Ming, Do you have the latest Apple updates? The latest is up to 10.5.6. They fixed a lot of stuff related to X11. Nick On Sat,

Re: [Freesurfer] cropping of average T1

2009-01-26 Thread Nick Schmansky
Sid, What is the field-of-view size? Use: mri_info orig.mgz and look for the 'fov' output. It should be 256. What is the fov of the input files in subj/mri/orig? If it is greater than 256, that might be the problem, but the cropping problem we have seen with that occurs during the original

Re: [Freesurfer] DODS/DOSS choice in patient/control study

2009-01-26 Thread Michael Harms
Hi Rysia, Doug, I'll just chime in that a fundamental decision you have to make is whether you want a statistical model that includes interaction terms. If you have 1 group factor (GRP) and 1 continuous covariate (COVAR1), a DODS model is essentially (using SAS shorthand): Y = GRP GRP*COVAR1

Re: [Freesurfer] Minor issues with Freesurfer v4.0.4/rerunning on 4.2.0

2009-01-26 Thread Nick Schmansky
John, If you're using the ?h-cerebral-white-matter stats in the aseg.stats files, or any of the data in the wmparc.stats file, then you will want to rerun recon-all -segstats -wmparc. If you're not using the ?h- cerebral-white-matter stats in the aseg.stats file, then you dont need to rerun.

Re: [Freesurfer] Qdec Cluster Size

2009-01-26 Thread Nick Schmansky
Miranda, I'll assume for now that what you mean by 'cluster' is not a cluster in the sense of clusters produced by a cluster-based correction for multiple comparisons, which was only very recently introduced to qdec (actually, just a script generator is produced). But rather, I think you mean