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Freeze config files for processing on compute canada: graham (#73)
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* - parameter config files for processing on graham

* - change username in sbatch account

* - change dataset name in config_sct_run_batch

* - change account and mail in job template

* - add emailing to job template

* remove mail-type END
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PaulBautin authored Sep 8, 2020
1 parent d093b6c commit 64d99c1
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Showing 4 changed files with 22 additions and 15 deletions.
18 changes: 8 additions & 10 deletions config_script.yml → config_script_t2.yml
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Expand Up @@ -3,21 +3,19 @@
# process_data.sh
# ---------------
# Number of transformations to apply to each subject
n_transfo: 2
n_transfo: 30
# Rescaling factor to apply to each subject. Note: value '1' should always be present.
rescaling:
- 1
- 0.99
- 0.98
- 0.97
- 0.96
- 0.95
- 0.94
- 0.93
# Contrasts on which to perform the analysis. Available values are: 't1', 't2'
contrast: "t1"
transfo_file: transfo_values.csv

# manual_labeling_correction.sh
# -----------------------------
# TODO: fetch path_output from yml config input to sct_run_batch
PATH_ORIGINAL_RESULTS: "csa_atrophy_results/results"
PATH_ORIGINAL_CSV: "csa_atrophy_results/data_processed"
PATH_DESTINATION_RESULTS: "csa_atrophy_results_corrected/results"
contrast: "t2"

# csa_atrophy_stat.py
# -------------------
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8 changes: 4 additions & 4 deletions config_sct_run_batch.yml
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@@ -1,8 +1,8 @@
# config file for sct_run_batch
path_data: spinegeneric_r20200801
path_output: csa_atrophy_results
script: process_data.sh
script_args: config_script.yml
path_data: /scratch/pabaua/data-multi-subject-p
path_output: /scratch/pabaua/results_csa_t2
script: /home/pabaua/csa-atrophy/process_data.sh
script_args: /home/pabaua/csa-atrophy/config_script_t2.yml
jobs: -1
batch_log: sct_run_batch_log.txt
continue_on_error: 1
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9 changes: 9 additions & 0 deletions job_template.sh
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@@ -0,0 +1,9 @@
#SBATCH --account=def-jcohen
#SBATCH --time=0-08:00 # time (DD-HH:MM)
#SBATCH --nodes=1
#SBATCH --cpus-per-task=32 # number of OpenMP processes
#SBATCH --mem=128G
#SBATCH [email protected]
#SBATCH --mail-type=ALL

cd $SCRATCH
2 changes: 1 addition & 1 deletion run_all.py
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Expand Up @@ -71,7 +71,7 @@ def main():
path_job_template = os.path.abspath(os.path.expanduser(arguments.job_template))
job_template = open(path_job_template, 'r').read()
else:
job_template = """#SBATCH --account=def-jcohen
job_template = """#SBATCH --account=def-pabaua
#SBATCH --time=0-08:00 # time (DD-HH:MM)
#SBATCH --nodes=1
#SBATCH --cpus-per-task=32 # number of OpenMP processes
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