singularity_commands.txt

singularity shell --bind \
    /media/DOCUMENTS/DOCUMENTS/MRI_ANALYSIS/pypreclin:/pypreclin \
    --bind /opt/jip:/jip \
    --bind $FSLDIR:/fsl \
    ./singularity/pypreclin-ubuntu.simg

FSLDIR=/fsl

python3


====

from pypreclin.workflow.preproc_fmri import preproc
from pprint import pprint
import os

rootdir = "/pypreclin/testdata"
funcfile = os.path.join(rootdir, "sub-danny_ses-20191219_run-01.nii.gz")
anatfile = os.path.join(rootdir, "sub-danny_ref_anat_res-0.5x0.5x0.5.nii.gz")
sid = "danny"
tr = "2.5"
outdir = "/pypreclin/testdata/output"
template = os.path.join(rootdir, "NMT.nii.gz")
jipdir = "/jip/bin"

--------

outputs = preproc(
        funcfile=funcfile,
        anatfile=anatfile,
        sid=sid,
        outdir=outdir,
        repetitiontime=tr,
        template=template,
        jipdir=jipdir,
        erase=False,
        resample=False,
        interleaved=False,
        sliceorder="ascending",
        realign_dof=6,
        realign_to_vol=True,
        warp=False,
        warp_njobs=1,
        warp_index=8,
        warp_file=None,
        warp_restrict=[0, 1, 0],
        delta_te=None,
        dwell_time=None,
        manufacturer=None,
        blip_files=None,
        blip_enc_dirs=None,
        unwarp_direction=None,
        phase_file=None,
        magnitude_file=None,
        anatorient="RAS",
        funcorient="RAS",
        kernel_size=3,
        fslconfig="/etc/fsl/5.0.11/fsl.sh",
        normalization_trf=None,
        coregistration_trf=None,
        recon1=False,
        recon2=False,
        auto=True,
        verbose=2)
pprint(outputs)