fMRIPrep Bootcamp | Day 1 :: Apptainer in UNIGE's HPC

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<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-06-apptainer/">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 20%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/day1-06-apptainer/
</a>

## Hands-on: Apptainer in UNIGE's HPC

Chris Markiewicz <<code>markiewicz@stanford.edu</code>>

Oscar Esteban <<code>phd@oscaresteban.es</code>>
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 Day 1 :: Apptainer in UNIGE's HPC

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# First SBATCH file

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Running *MRIQC* on the anatomical T1w images:
``` Bash
#!/bin/bash
#SBATCH --time=1:00:00 #NOTE: likely longer than generally needed 
#SBATCH --ntasks 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=1G
#SBATCH --partition=shared-cpu
#SBATCH --reservation=share_courvoisier_workshop_570

# Outputs ----------------------------------
#SBATCH --output log/%x-%A-%a.out
#SBATCH --error log/%x-%A-%a.err
#SBATCH --mail-user=phd@oscaresteban.es
#SBATCH --mail-type=ALL
# ------------------------------------------

srun apptainer run mriqc_latest.sif \
     $HOME/ds005454/ $HOME/derivatives/mriqc-24.0.2 participant \
     -m T1w -vv --dsname bootcamp --nprocs 12 --omp-nthreads 8

```

Run with:
``` Bash
$ sbatch mriqc.sbatch
```
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# The `srun` call

### 1 | apptainer run

``` Bash
srun apptainer run mriqc_latest.sif \
```

### 2 | BIDS-Apps' interface

Reminder: `<bids-app-name> /input-data /output-folder participant`
``` Bash
 $HOME/ds005454/ $HOME/derivatives/mriqc-24.0.2 participant \
```

### 3 | MRIQC's specific arguments

We only run T1w images (`-m T1w`), we make it more verbose `-vv`,
we name the dataset (`--dsname bootcamp`), we allow the workflow
to run up to 16 processes with up to 8 cores each `--nprocs 16 --omp-nthreads 8`:
``` Bash
     -m T1w -vv --dsname bootcamp --nprocs 16 --omp-nthreads 8
```