This preproc script
#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
=============================================
fMRI: OpenfMRI.org data, FSL, ANTS, c3daffine
=============================================
A growing number of datasets are available on `OpenfMRI <http://openfmri.org>`_.
This script demonstrates how to use nipype to analyze a data set::
python fmri_ants_openfmri.py --datasetdir ds107
"""
from nipype import config
config.enable_provenance()
import six
from glob import glob
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# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from __future__ import division
import os
from ....interfaces import fsl as fsl # fsl
from ....interfaces import utility as util # utility
from ....pipeline import engine as pe # pypeline engine
from ....interfaces import freesurfer as fs # freesurfer
from ....interfaces import spm as spm
from ...smri.freesurfer.utils import create_getmask_flow
from .... import LooseVersion
def getthreshop(thresh):
return ['-thr %.10f -Tmin -bin' % (0.1 * val[1]) for val in thresh]
def pickrun(files, whichrun):
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I’d like to remove Susan smoothing and instead use the Smooth node from here:
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Provides interfaces to various commands provided by FreeSurfer
"""
from __future__ import (print_function, division, unicode_literals,
absolute_import)
from builtins import range
import os
import os.path as op
from glob import glob
import shutil
import numpy as np
from nibabel import load
from ... import logging, LooseVersion
from ...utils.filemanip import fname_presuffix, check_depends
from ..io import FreeSurferSource
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but the smooth node requires a register.dat. As I understand it, register.dat is created by fmri_ants_bids.py but not until after preprocessing has occured. Do I need to run the script twice in order to get that reg.dat or am I missing something?