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Remove dead link to Dockerfile from Nipoppy MRIQC page #89

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Sep 21, 2023
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14 changes: 8 additions & 6 deletions docs/nipoppy/workflow/proc_pipe/mriqc.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,17 @@ MRIQC processes the participants and produces image quality metrics from T1w, T2


### [MRIQC](https://mriqc.readthedocs.io/en/latest/)
- Ensure you are running the appropriate MRIQC image, as provided [here](https://github.com/neurodatascience/nipoppy/blob/main/workflow/proc_pipe/mriqc/Dockerfile)
- Use [run_mriqc.py](https://github.com/neurodatascience/nipoppy/tree/main/workflow/proc_pipe/mriqc) to run MRIQC pipeline directly or wrap the script in an SGE/Slurm script to run on cluster

```bash
python run_mriqc.py --global_config CONFIG.JSON --subject_id 001 --output_dir OUTPUT_DIR_PATH
- Mandatory: Pass in the absolute path to the configuration containing the MRIQC container and data directory to `global_config`
- Mandatory: Pass in the subject id to `participant_id`
- Mandatory: Pass in the subject id to `session_id`
- Mandatory: Pass in the absolute path to the output directory to `output_dir`

```

- Mandatory: Pass in the absolute path to the configuration containing the MRIQC container and data directory to `global_config`
- Mandatory: Pass in the subject id to `participant_id`
- Mandatory: Pass in the subject id to `session_id`
- Mandatory: Pass in the absolute path to the output directory to `output_dir`

!!! note
An example config is located [here](https://github.com/neurodatascience/nipoppy/blob/main/sample_global_configs.json)

Expand Down