Re: [Freesurfer] Run Recon-all Parallel on Linux

2020-01-04 Thread Tim Schäfer
External Email - Use Caution Hi Frank, The OS shouldn't make any difference as long as you use the same shell. You will have to install GNU parallel first as it's usually not installed by default under Linux (on Debian-based distros: `sudo apt-get install parallel`). I have she

Re: [Freesurfer] Run Recon-all Parallel on Linux

2020-01-04 Thread Bruce Fischl
Hi Frank in Linux you would just add an & to the end of the recon-all command line to put it in the background and start however many you want. Or you can run them from different terminal windows. If you have a lot to get through you can do something like (note this is not debugged!): set ma

Re: [Freesurfer] Getting issue in running bt_recon

2020-01-04 Thread Bruce Fischl
Hi Sudhakar if you want us to help you we will need a lot more information. What exact command did you run? What was the entire screen output? What kind of computer are you running it on? That kind of thing cheers Bruce On Sat, 4 Jan 2020, sudhakar Mishra wrote: External Email -

[Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?

2020-01-04 Thread Mohammad Rashid
External Email - Use Caution I recently ran this command: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cereb