diff --git a/generate.sh b/generate.sh index a22ace7..ca87608 100644 --- a/generate.sh +++ b/generate.sh @@ -17,7 +17,7 @@ generate_docker() { --miniconda \ conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \ - pip_install="https://github.com/nipy/nipype/tarball/master + pip_install="git+https://github.com/nipy/nipype.git@rel/1.6.1 https://github.com/INCF/pybids/tarball/0.7.1 nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \ create_env="neuro" \ @@ -56,7 +56,7 @@ generate_singularity() { --miniconda \ conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \ - pip_install="https://github.com/nipy/nipype/tarball/master + pip_install="git+https://github.com/nipy/nipype.git@rel/1.6.1 https://github.com/INCF/pybids/tarball/0.7.1 nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \ create_env="neuro" \ diff --git a/notebooks/basic_nodes.ipynb b/notebooks/basic_nodes.ipynb index b8e2627..20cdbfe 100644 --- a/notebooks/basic_nodes.ipynb +++ b/notebooks/basic_nodes.ipynb @@ -170,8 +170,10 @@ "metadata": {}, "outputs": [], "source": [ + "in_file = '/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz'\n", + "\n", "# Specify node inputs\n", - "bet.inputs.in_file = '/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz'\n", + "bet.inputs.in_file = in_file\n", "bet.inputs.out_file = '/output/node_T1w_bet.nii.gz'" ] }, @@ -200,7 +202,7 @@ "from nilearn.plotting import plot_anat\n", "%matplotlib inline\n", "import matplotlib.pyplot as plt\n", - "plot_anat(bet.inputs.in_file, title='BET input', cut_coords=(10,10,10),\n", + "plot_anat(in_file, title='BET input', cut_coords=(10,10,10),\n", " display_mode='ortho', dim=-1, draw_cross=False, annotate=False);\n", "plot_anat(res.outputs.out_file, title='BET output', cut_coords=(10,10,10),\n", " display_mode='ortho', dim=-1, draw_cross=False, annotate=False);"