Re: [Freesurfer] Change the default SUBJECTS_DIR...

2011-04-22 Thread Bruce Fischl
Hi Catherine, you can save your data whereever you want. You can also set it directly on the recon-all command line with -sd . Are you running in a virtual box? What is the path to your usb drive in it? Probably not E:\... cheers Bruce On Fri, 22 Apr 2011, Rongxiang Tang wrote: Dear A

[Freesurfer] Change the default SUBJECTS_DIR...

2011-04-22 Thread Rongxiang Tang
Dear All, All my data is on a USB hard drive and I do not want to put them in the "/home/virtualuser/apps/freesurfer/subjects" directory, which is the default... Also, I would like to save all my results on that USB hard drive... I was wondering if I would be able to do that... I tried this: Fre

[Freesurfer] No inflated brain...

2011-04-22 Thread jim kroger
Hello, I am following the sequence in the "FreeSurfer Troubleshooting Reconstruction Work Flow" instructions, and am at step 8, FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus callosum are included as white matter, and the pial surface surrounds some subcortical structures. Assum

Re: [Freesurfer] Could I run several freesurfers at the same time?

2011-04-22 Thread Gergely Orsi
For the first part, yes it's good. Give it 3 cores and at least 6GB of memory (~6144MB, but 6028 will be fine), but you can also give it 9GB as others suggested, as you have plenty and won't miss it. :) For the second part, also yes. Open 3 terminal windows, and use separate commands in each. Now