Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Lea, sorry for the late reply, just in case this is still of interest: 1. It is possible to process all cross data with 5.3 and then base and long with 6.0. As long as you do the same for all subjects it should be fine, just don't mix across subjects. Also depending on the size if only

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Could be all that is needed is to add this: mycluster ='sbatch --mail-type=FAIL --mail-user= -N 1 --ntasks-per-node=10 --partition=work --export=ALL -o /%(username)s/logs/job.%J.out- e /%(username)/logs/job.%J.err "%(command)s"' and comment the lines # if queue is not None ... # pbcmd =

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

hi lea, in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer and then submit each subject's longitudinal pipeline as a separate slurm job. cheers, satra On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter wrote:

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed}

Hi Lea, I wrote that script to simplify processing on our cluster which uses qsub PBS for submission. I have never used SLURM so far. There is two functions that you (or someone who knows this stuff) would need to modify: def submit and def wait_jobs The submit procedure basically