diff --git a/docs/TUTORIAL.md b/docs/TUTORIAL.md index 9cd54ef..5835caf 100644 --- a/docs/TUTORIAL.md +++ b/docs/TUTORIAL.md @@ -583,6 +583,8 @@ Consult `wm_apply_ORG_atlas_to_subject.sh --help` to know the details of these p Run it: +##### Through Luigi pipeline + ```bash export LUIGI_CONFIG_PATH=/path/to/dwi_pipe_params.cfg @@ -590,6 +592,40 @@ exec/ExecuteTask --task Wma800 \ --bids-data-dir /data/pnl/DIAGNOSE_CTE_U01/rawdata -c 1001 --dwi-template sub-*/ses-01/dwi/*_dwi.nii.gz ``` +##### On a PNL workstation physically or through NoMachine + +``` +NEW_SOFT_DIR=/rfanfs/pnl-zorro/software/pnlpipe3/ +source ${NEW_SOFT_DIR}/bashrc3 + +wm_apply_ORG_atlas_to_subject.sh \ +-i /path/to/your.vtk \ +-o /path/to/output/dir/ \ +-a ${NEW_SOFT_DIR}/ORG-Atlases-1.2 \ +-s ${NEW_SOFT_DIR}/Slicer-4.10.2-linux-amd64/SlicerWithExtensions.sh \ +-m "${NEW_SOFT_DIR}/Slicer-4.10.2-linux-amd64/SlicerWithExtensions.sh --launch FiberTractMeasurements" \ +-n 8 -c 2 -d 1 +``` + +The same command applies for running it on PNL's GRX node: `dna007.partners.org` except a change in the software directory: + +> NEW_SOFT_DIR=/data/pnl/soft/pnlpipe3/ + + +##### Through SSH + +Just append the `-x 1` flag to the above command to enable virtual X server: + +``` +wm_apply_ORG_atlas_to_subject.sh \ +... +-n 8 -c 2 -d 1 -x 1 +``` + +However, running it through SSH requires availability of `xvfb-run` on that server--may it be a PNL workstation or a GRX node. +The good news is that we have already installed `xorg-x11-server-Xvfb` in most servers. So you should be all set. +But if you find `xvfb-run`'s absence, reach out to PNL engineers for help. + # Fs2Dwi pipeline