pypreprocess

pypreprocess is a collection of python scripts for preprocessing fMRI data (motion correction, spatial normalization, smoothing, ...). It provides:

• the possibility to run processing pipelines using simple text-based configuration-files, allowing to analyse data without programming;
• automatic generation of html reports, for example for quality assurance (e.g. spatial registration checks), statistical results, etc.;
• parallel processing of multiple subjects on multi-core machines;
• persistence of intermediate stages: in case an analysis is interrupted, cached intermediates files are reused to speed up processing;
• support for precompiled SPM (besides the usual matlab-dependent flavor).

pypreprocess relies on nipype's interfaces to SPM (both precompiled SPM and matlab-dependent SPM flavors). It also has pure-Python (no C extensions, no compiled code, just Python) modules and scripts for slice-timing correction, motion correction, coregistration, and smoothing, without need for nipype or matlab. It has been developed in the Linux environment and is tested with Ubuntu 16 and 18. No guarantees with other OSes.

License

All material is Free Software: BSD license (3 clause).

Important links

• Official source code repo: https://github.com/neurospin/pypreprocess

Dependencies

• Python >= 3.5
• Numpy >= 1.11
• SciPy >= 0.19
• Scikit-learn >= 0.19
• matplotlib >= 1.5.1
• nibabel >= 2.0.2
• nipype >= 1.4
• configobj >= 5.0.6
• nilearn >= 0.6.2
• Pandas >= 0.23

Installation

To begin with, you may also want to install the pre-compiled version of SPM (in case you don't have matlab, etc.). From the main pypreprocess directory, run the following:

$ . continuous_integration/install_spm12.sh

Second, install the python packages pip, scipy, pytest, nibabel, scikit-learn, nipype, pandas, matplotlib, nilearn and configobj. If you have a python virtual environment, just run:

$ pip install scipy scikit-learn nibabel nilearn configobj coverage pytest matplotlib pandas nipype

If not, make sure to install pip (run: 'sudo apt-get install python-pip'). If you want to install these locally, use the --user option:

$ pip install scipy scikit-learn nibabel nilearn configobj coverage pytest matplotlib pandas nipype --ignore-installed --user

If you want to install these for all users, use sudo:

$ pip install scipy scikit-learn nibabel nilearn configobj coverage pytest matplotlib pandas nipype --ignore-installed

Finally, install pypreprocess itself by running the following in the pypreprocess:

$ python setup.py install --user

or simply 'python setup.py install' in a virtual environment.

After Installation: Few steps to configure SPM on your own device

There are three cases:

• If you have used the pypreprocess/continuous_integration/setup_spm.sh or install_spm script, you have nothing to do.

• If you have matlab and spm installed, then specify the location of your SPM installation directory and export this location as SPM_DIR:

  $ export SPM_DIR=/path/to/spm/installation/dir
  

• If you have installed a pre-compiled version of SPM then, specify the location of the SPM executable and export as SPM_MCR:

  $ export SPM_MCR=/path/to/spm_mcr_script (script implies spm12.sh)
  

Getting started: pypreprocess 101

Simply cd to the examples/easy_start/ sub-directory and run the following command:

$ python nipype_preproc_spm_auditory.py

If you find nipype errors like "could not configure SPM", this is most likely that the export of SPM_DIR and SPM_MCR (see above) have not been done in this shell.

Layout of examples

We have written some example scripts for preprocessing some popular datasets. The examples directory contains a set of scripts, each demoing an aspect of pypreprocessing. Some scripts even provide use-cases for the nipy-based GLM. The examples use publicly available sMRI and fMRI data. Data fetchers are based on the nilearn API. The main examples scripts can be summarized as follows:

Very easy examples

• examples/easy_start/nipype_preproc_spm_auditory.py: demos preprocessing + first-level GLM (using nipy) on the single-subject SPM auditory dataset.
• examples/easy_start/nipype_preproc_spm_haxby.py: preprocessing of the 'Haxby2001' visual recognition task fMRI dataset.

More advanced examples

• examples/pipelining/nipype_preproc_spm_multimodal_faces.py: demos preprocessing + first-level fixed-effects GLM on R. Henson's multi-modal face dataset (multiple sessions)
• examples/pipelining/nistats_glm_fsl_feeds_fmri.py: demos preprocessing + first-level GLM on FSL FEEDS dataset using nistats python package.

Examples using pure Python (no SPM, FSL, etc. required)

• examples/pure_python/slice_timing_demos.py, examples/pure_python/realign_demos.py, examples/pure_python/coreg_demos.py: demos Slice-Timing Correction (STC), motion-correction, and coregistration on various datasets, using modules written in pure Python
• examples/pure_python/pure_python_preproc_demo.py: demos intra-subject preprocessing using pure Python modules, on single-subject SPM auditory dataset

Using .ini configuration files to specify pipeline

It is possible (and recommended) to configure the preprocessing pipeline just by copying any of the .ini configuration files under the examples sub-directory and modifying it (usually, you only need to modify the dataset_dir parameter), and then run:

$ python pypreprocess.py your.ini

For example,:

$ python pypreprocess.py examples/easy_start/spm_auditory_preproc.ini

Pipelines

We have put in place two main pipelines for preprocessing: the standard pipeline, and the DARTEL-based pipeline. In the end of either method, each subject's EPI data has been corrected for artefacts, and placed into the same reference space (MNI). When you invoke the do_subjects_preproc(..) API of [nipype_preproc_spm_utils.py](https://github.com/neurospin/pypreprocess/blob/master/pypreprocess/nipype_preproc_spm_utils.py) to preprocess a dataset (group of subjects), the default pipeline used is the standard one; passing the option do_dartel=True forces the DARTEL-based pipeline to be used. Also you can fine-tune your pipeline using the the various supported parameters in you .ini file (see the examples/ subdirectory for examples).

Standard pipeline

For each subject, the following preprocessing steps are undergone:

• Motion correction is done to estimate and correct for subject's head motion during the acquisition.
• The subject's anatomical image is coregistered against their fMRI images (precisely, to the mean thereof). Coregistration is important as it allows deformations of the anatomy to be directly applicable to the fMRI, or for ROIs to be defined on the anatomy.
• Tissue Segmentation is then employed to segment the anatomical image into GM, WM, and CSF compartments by using TPMs (Tissue Probability Maps) as priors.
• The segmented anatomical image are then warped into the MNI template space by applying the deformations learned during segmentation. The same deformations have been applied to the fMRI images.

DARTEL pipeline

Motion correction, and coregistration go on as for the standard pipeline. The only difference between the DARTEL pipeline and the standard one is the way the subject EPI are warped into MNI space.

In the "Dartel pipeline", SPM's [DARTEL](http://www.fil.ion.ucl.ac.uk/spm/software/spm8/SPM8_Release_Notes.pdf) is used to warp subject brains into MNI space.

• The idea is to register images by computing a “flow field” which can then be “exponentiated” to generate both forward and backward deformations. Processing begins with the “import” step. This involves taking the parameter files produced by the segmentation (NewSegment), and writing out rigidly transformed versions of the tissue class images, such that they are in as close alignment as possible with the tissue probability maps.
• The next step is the registration itself. This involves the simultaneous registration of e.g. GM with GM, WM with WM and 1-(GM+WM) with 1-(GM+WM) (when needed, the 1- (GM+WM) class is generated implicitly, so there is no need to include this class yourself). This procedure begins by creating a mean of all the images, which is used as an initial template. Deformations from this template to each of the individual images are computed, and the template is then re-generated by applying the inverses of the deformations to the images and averaging. This procedure is repeated a number of times.
• Finally, warped versions of the images (or other images that are in alignment with them) can be generated.

[nipype_preproc_spm_abide.py](https://github.com/neurospin/pypreprocess/blob/master/scripts/abide_preproc.py) is a script which uses this pipeline to preprocess the [ABIDE](http://fcon_1000.projects.nitrc.org/indi/abide/).

Intra-subject preprocessing in pure Python (with no compiled code, etc.)

A couple of modules for intra-subject preprocessing (slice-timing correction, motion-correction, coregistration, etc.) in pure (only using builtins and numpy/scipy official stuff, no compiled code, no wrappers) Python have been implemented. To demo this feature, simply run the following command:

$ python examples/pure_python/pure_python_preproc_demo.py

Development

You can check the latest version of the code with the command:

$ git clone git://github.com/neurospin/pypreprocess.git

or if you have write privileges:

$ git clone git@github.com:neurospin/pypreprocess.git

• whitespaces in the directory name for the variable 'scratch' triggers a bug in nipype and results in a crash (have not tested if this also occur for other path variables)
• when using an 'ini' file, say 'mytest.ini', with ''python preprocessing.py mytest.ini'', there can be a conflict between pypreprocess.py and the pypreprocess module (solution: rename pypreprocess.py into something like pypreprocini.py)
• the cache is not relocatable (because joblib encode the absolute paths): if you are forced to move the cache -- e.g. because of lack of space on a filesystem -- use a symbolic link to let the system believe that the cache is still at the original location.