Initial commit

init.sh

+#!/bin/bash
+
+export FSLDIR="$HOME/fsl" # Change according to the user's FSL installation
+export BB_BIN_DIR="$HOME/BIP/" # Change according to the present folder
+export PATH="$BB_BIN_DIR:$BB_BIN_DIR/data:$BB_BIN_DIR/bb_pipeline:$PATH"
+export PYTHONPATH="$BB_BIN_DIR:$PYTHONPATH"

install_dir/.gitignore

+.DS_Store
+list_*.txt

install_dir/manual_install.txt

+
+# Installing FSL (with its own miniconda)
+curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py > fslinstaller.py
+python ./fslinstaller.py --no_env --dest $HOME/fsl/
+export FSLDIR="$HOME/fsl"
+export PATH="$FSLDIR/bin/:$PATH"
+pushd $FSLDIR
+git clone https://git.fmrib.ox.ac.uk/fsl/fslpy
+cd fslpy
+$FSLDIR/bin/pip install -e .
+popd
+rm -f ./fslinstaller.py
+
+# Creating a new python environment
+$FSLDIR/bin/conda create -n ukb python=3.10
+source $FSLDIR/bin/activate ukb
+pip install file-tree file-tree-fsl
+pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/pipe-tree.git
+pip install -r $BB_BIN_DIR/install_dir/requirements.txt
+pip list &>  $BB_BIN_DIR/install_dir/list_`date +%Y_%m_%d`.txt
+
+# Install gradunwarp
+tar -zxvf gradunwarp_FMRIB.tar.gz
+cd gradunwarp_FMRIB
+python setup.py install
+cd ..
+rm -rf gradunwarp_FMRIB

install_dir/requirements.txt

+oxasl
+oxasl-deblur
+pickle-mixin
+Babel
+Jinja2
+MarkupSafe
+Pillow
+PyWavelets
+Sphinx
+Theano
+bottom
+deprecation
+jupyter-core
+niicat
+nose
+pygam
+retrying
+simplegeneric
+graphviz
+pickleshare
+ipython
+seaborn
+jsonschema
+python-utils
+zipp
+urllib3
+scikit-image
+scikit-learn

install_dir/setup.py

+from setuptools import setup,find_packages
+with open('requirements.txt', 'rt') as f:
+    install_requires = [l.strip() for l in f.readlines()]
+
+setup(name='BIP',
+	version='1.0.0',
+	description='Brain Imaging Pipeline',
+	author='Fidel Alfaro Almagro',
+	install_requires=install_requires,
+    scripts=['BIP/general/BIP'],
+	packages=find_packages(),
+	include_package_data=True)

my_wrappers/.gitignore

+.DS_Store

my_wrappers/standard_space_roi.py

+#!/usr/bin/env python
+#
+# standard_space_roi.py - Wrapper for the standard_space_roi command.
+#
+# Author: Fidel Alfaro Almagro
+#
+"""This module provides the :func:`standard_space_roi` function, a wrapper for
+the FSL `standard_space_roi`_ command.
+"""
+
+import fsl.utils.assertions as asrt
+from   fsl.wrappers import wrapperutils  as wutils
+
+@wutils.fileOrImage('input', 'maskMASK', 'roiMASK', 'ssref', 'altinput',outprefix='output')
+@wutils.fslwrapper
+def standard_space_roi(input, output, **kwargs):
+    """Wrapper for the ``standard_space_roi`` command.
+
+    :arg maskFOV:   Mask output using transformed standard space FOV (default)
+    :arg maskMASK:  Mask output using transformed standard space mask
+    :arg maskNONE:  Do not mask output
+
+    :arg roiFOV:    Cut down input FOV using bounding box of the transformed standard space FOV (default)
+    :arg roiMASK:   Cut down input FOV using nonbackground bounding box of the transformed standard space mask
+    :arg roiNONE:   Co not cut down input FOV
+
+    :arg ssref      Standard space reference image to use (default $FSLDIR/data/standard/MNI152_T1)
+    :arg altinput   Alternative input image to apply the ROI to (instead of the one used to register to the reference)
+    :arg d          Debug (don't delete intermediate files)
+    :arg b          Betpremask, equivalent to: -maskMASK $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil -roiNONE
+
+    Refer to the ``standard_space_roi`` command-line help for details on all arguments.
+    """
+    asrt.assertIsNifti(input)
+
+    valmap = {
+        'maskFOV' : wutils.SHOW_IF_TRUE,
+        'maskNONE' : wutils.SHOW_IF_TRUE,
+        'roiFOV' : wutils.SHOW_IF_TRUE,
+        'roiNONE' : wutils.SHOW_IF_TRUE,
+        'd' : wutils.SHOW_IF_TRUE,
+        'b' : wutils.SHOW_IF_TRUE,
+    }
+
+    cmd  = ['standard_space_roi', input, output]
+
+    cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs)
+
+    return cmd