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Add SCFSL GPU to Usage docs
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pcamach2 committed Mar 15, 2022
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Expand Up @@ -65,6 +65,32 @@ Step 3 - diffusion MRI stream
sbatch -a 001,002,003 ./dyno_PROJ_A.sh slurm_proc_7T_CUPS_step3.sh <PROJECTID> <base directory> <version>
(Optional) Running FreeSurfer-informed FSL DTI tractography on GPU
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.. note::
Requires pre-existing FreeSurfer parcellation and FreeSurfer license.txt.
As of 03/15/2022, the main pipeline will can produce the QSIPrep preprocessing outputs in fsl space for this workflow.
*These QSIPrep preprocessing outputs are required for the current script!*
This workflow is intended to run on machines with CUDA 9.1 or CUDA 10.2 compatible GPUs.

*Docker*

.. code-block:: bash
# Running SCFSL GPU tractography
docker exec --gpus all -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64 \
-v /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt \
-v /path/project/bids:/data mrfilbi/scfsl_gpu:0.3.2 /bin/bash /scripts/proc_fsl_connectome_fsonly.sh ${subject} ${session}
*Singularity*

.. code-block:: bash
# Running SCFSL GPU tractography
SINGULARITY_ENVLD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64 \
singularity exec --nv -B /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt,/path/project/bids:/data \
/path/to/scfsl_gpu-v0.3.2.sif /bin/bash /scripts/proc_fsl_connectome_fsonly.sh ${subject} ${session}
Metrics Collation
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