Removing some remaining old files

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