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Artemis job submission examples
- Chengtao Liang (Unlicensed)
- Sophie Matis
This page will show examples of different job submissions. Please refer to official Artemis documentation on job submission if you wish to understand the basics and explanation of the commands.
Submitting a job on a single subject
Example of running recon-all on FreeSurfer on a single subject (FTD001).
Save the following script as a .pbs script. (e.g. reconall.pbs)
#!/bin/bash -v
#PBS -P NeuroBMC
#PBS -N FreeSurfer_reconall
#PBS -l select=1:ncpus=4:mem=16GB
#PBS -l walltime=24:00:00
#PBS -q defaultQ
$PBS_O_WORKDIR
module load freesurfer/7.1.0
module load mrtrix3/3.0.1
cd /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched
export SUBJECTS_DIR=/scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched
mrconvert /path/to/dicom/FTD001 /path/to/niftii/FTD001.nii -strides -1,2,3
recon-all -sd /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched -subjid FTD001 -i /path/to/niftii/FTD001.nii -all
2. Run on Artemis by using qsub in the terminal
qsub reconall.pbsSubmitting a job on multiple subjects (in parallel)
Example of running a recon-all script on FreeSurfer across multiple subjects.
Set up your folders so every subject has the same folder structure. Basically, this script will just replace your subject name ‘FTD001’ and repeat the same command while only changing the subject name ‘FTD001’ for each subject. So you need to make sure your subjects are in same path, e.g. /path/to/folder/FTD####.
Create a .pbs file, replacing the subject (e.g. FTD001) with ${sub}
#!/bin/bash -v
#PBS -P NeuroBMC
#PBS -N FreeSurfer_reconall
#PBS -l select=1:ncpus=4:mem=16GB
#PBS -l walltime=24:00:00
#PBS -q defaultQ
$PBS_O_WORKDIR
module load freesurfer/7.1.0
module load mrtrix3/3.0.1
cd /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched
export SUBJECTS_DIR=/scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched
mrconvert /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched/DICOM/${sub} /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched/niftii/${sub}_T1w.nii -strides -1,2,3
recon-all -sd /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched -subjid ${sub} -i /scratch/NeuroBMC/Cheng/DWI_mrtrix_longitudinal/Matched/niftii/${sub}_T1w.nii -all
3. Go to Artemis on terminal and add your subject IDs to a list.
Tip: Instead of typing each subject itself, you can use the ‘ls’ command on a folder with all your subject inside (list = ls 'nameofyoursubjectfolder').
4. Submit the jobs via a ‘for loop’ in the Artemis terminal: