neurospin · SylvainLan · Feb 14, 2018 · Feb 14, 2018 · Feb 14, 2018
diff --git a/examples/easy_start/nipype_preproc_spm_auditory.py b/examples/easy_start/nipype_preproc_spm_auditory.py
@@ -1,6 +1,7 @@
 """
-Author: dohmatob elvis dopgima elvis[dot]dohmatob[at]inria[dot]fr
-Synopsis: Minimal script for preprocessing single-subject data
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
+:Synopsis: Minimal script for preprocessing single-subject data
+
 """
 
 import os

diff --git a/examples/easy_start/nipype_preproc_spm_haxby.py b/examples/easy_start/nipype_preproc_spm_haxby.py
@@ -1,6 +1,7 @@
 """
-Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
-Synopsis: Preprocessing of HAXBY 2001 dataset
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
+:Synopsis: Preprocessing of HAXBY 2001 dataset
+
 """
 
 import os

diff --git a/examples/easy_start/segmentation_demos.py b/examples/easy_start/segmentation_demos.py
@@ -1,10 +1,9 @@
 # -*- coding: utf-8 -*-
 """
-Demo script for anatomical MRI segmentation with SPM.
-
+:Synopsis: Demo script for anatomical MRI segmentation with SPM.
 It demos segmentations on SPM single-subject auditory.
+:Author: RAHIM Mehdi
 
-@author: Mehdi RAHIM
 """
 
 import os

diff --git a/examples/pipelining/nipype_preproc_spm_multimodal_faces.py b/examples/pipelining/nipype_preproc_spm_multimodal_faces.py
@@ -1,7 +1,8 @@
 """
-:Author: yannick schwartz, dohmatob elvis dopgima
 :Synopsis: Minimal script for preprocessing single-subject data
 + GLM with nistats
+:Author: SCHWARTZ Yannick, DOHMATOB Elvis Dopgima
+
 """
 
 # standard imports

diff --git a/examples/pipelining/nipype_preproc_spm_nyu.py b/examples/pipelining/nipype_preproc_spm_nyu.py
@@ -1,6 +1,7 @@
 """
-:Author: DOHMATOB Elvis Dopgima
 :Synopsis: Preprocessing of NYU rest data.
+:Author: DOHMATOB Elvis Dopgima
+
 """
 
 import sys

diff --git a/examples/pipelining/nistats_glm_fsl_feeds_fmri.py b/examples/pipelining/nistats_glm_fsl_feeds_fmri.py
@@ -1,7 +1,8 @@
 """
-Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
 Synopsis: Demo script for nipy's GLM and inference + reporting
 on FSL's FEEDS fMRI single-subject example data
+Author: DOHMATOB Elvis Dopgima
+
 """
 
 import os

diff --git a/examples/pipelining/openfmri_preproc.py b/examples/pipelining/openfmri_preproc.py
@@ -1,6 +1,6 @@
 """
-Author: yannick schwartz, DOHMATOB Elvis Dopgima
-Synopsis: Command line interface to preprocess OpenfMRI
+:Synopsis: Command line interface to preprocess OpenfMRI
+:Author: SCHWARTZ Yannick , DOHMATOB Elvis Dopgima
 """
 
 import os

diff --git a/examples/pure_python/coreg_demos.py b/examples/pure_python/coreg_demos.py
@@ -1,9 +1,9 @@
 """
-Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
-Synopsis: Demo for coregistration in pure python
+:Synopsis: Demo for coregistration in pure python
 
 It demos coregistration on a variety of datasets including:
 SPM single-subject auditory, NYU rest, ABIDE, etc.
+:Author: DOHMATOB Elvis Dopgima
 """
 
 import os

diff --git a/examples/pure_python/pure_python_preproc_demo.py b/examples/pure_python/pure_python_preproc_demo.py
@@ -1,6 +1,6 @@
 """
-Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
-Synopsis: single_subject_pipeline.py demo
+:Synopsis: single_subject_pipeline.py demo
+:Author: DOHMATOB Elvis Dopgima
 """
 
 from pypreprocess.datasets import fetch_spm_multimodal_fmri

diff --git a/examples/pure_python/realign_demos.py b/examples/pure_python/realign_demos.py
@@ -1,6 +1,6 @@
 """
-Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
-Synopsis: single_subject_pipeline.py demo
+:Synopsis: single_subject_pipeline.py demo
+:Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
 """
 
 import os

diff --git a/examples/pure_python/slice_timing_demos.py b/examples/pure_python/slice_timing_demos.py
@@ -1,6 +1,6 @@
 """
-:Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
 :Synopsis: Manipulations with slice timing
+:Author: DOHMATOB Elvis Dopgima elvis[dot]dohmatob[at]inria[dot]fr
 """
 
 import sys

diff --git a/pypreprocess/affine_transformations.py b/pypreprocess/affine_transformations.py
@@ -1,7 +1,7 @@
 """
 :Module: affine_transformations
 :Synopsis: routine functions for doing affine transformation-related business
-:Author: DOHMATOB Elvis Dopgima
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 References
 ----------

diff --git a/pypreprocess/cluster_level_analysis.py b/pypreprocess/cluster_level_analysis.py
@@ -1,7 +1,8 @@
-""" Utilities to describe the result of cluster-level analysis of statistical
+"""
+:Synopsis: Utilities to describe the result of cluster-level analysis of statistical
 maps.
+:Author: THIRION Bertrand
 
-Author: Bertrand Thirion, 2015
 """
 import numpy as np
 from scipy.ndimage import label, maximum_filter

diff --git a/pypreprocess/configure_spm.py b/pypreprocess/configure_spm.py
@@ -1,7 +1,8 @@
 """
-Automatic configuration of MATLAB/SPM back-end
+:Synopsis: Automatic configuration of MATLAB/SPM back-end
+:Author: DOHMATOB Elvis Dopgima, SCHWARTZ Yanick, DOCKES Jerome
+
 """
-# author: Elvis DOHMATOB, Yanick SCHWARZ, Jerome DOCKES
 
 import os
 import re

diff --git a/pypreprocess/fsl_to_nistats.py b/pypreprocess/fsl_to_nistats.py
@@ -2,7 +2,7 @@
 :Module: fsl_to_nistats
 :Synopsis: Utility script for converting FSL configuration (design, etc.) files
 into Dataframe format.
-:Author: DOHMATOB Elvis Dopgima <[email protected]> <[email protected]>
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 """
 

diff --git a/pypreprocess/io_utils.py b/pypreprocess/io_utils.py
@@ -1,7 +1,6 @@
 """
-:Module: utils
 :Synopsis: routine business related to image i/o manips
-:Author: dohmatob elvis dopgima
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 """
 

diff --git a/pypreprocess/kernel_smooth.py b/pypreprocess/kernel_smooth.py
@@ -3,8 +3,8 @@
 :Synopsis: assorted utilities for smoothing images (to absorb noise before
 computing a gradient, etc.). A good starting point for understanding this code
 is the smooth_image(..) wrapper function
-:Author: DOHMATOB Elvis Dopgima, adapted from nipy source code. Credits
-to nipy dev.
+:Author: DOHMATOB Elvis Dopgima (adapted from nipy source code. Credits
+to nipy dev).
 
 """
 

diff --git a/pypreprocess/nipype_preproc_fsl_utils.py b/pypreprocess/nipype_preproc_fsl_utils.py
@@ -1,5 +1,5 @@
 """
-Author: Bertrand Thirion, Alexandre Abraham, DOHMATOB Elvis Dopgima
+:Author: THIRION Bertrand, ABRAHAM Alexandre, DOHMATOB Elvis Dopgima
 
 """
 

diff --git a/pypreprocess/nipype_preproc_spm_utils.py b/pypreprocess/nipype_preproc_spm_utils.py
@@ -1,10 +1,9 @@
 """
-Utility functions for single- and mult-subject preprocessing of fMRI
-
+:Synopsis: Utility functions for single- and mult-subject preprocessing of fMRI
 The most useful functions are do_subject_preproc and do_subjects_preproc
-"""
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
-# Author: DOHMATOB Elvis Dopgima <[email protected]>
+"""
 
 import os
 import sys

diff --git a/pypreprocess/realign.py b/pypreprocess/realign.py
@@ -1,7 +1,7 @@
 """
 :Module: spm_realign
 :Synopsis: MRI within-modality Motion Correction, SPM style
-:Author: DOHMATOB Elvis Dopgima
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 """
 

diff --git a/pypreprocess/reporting/check_preprocessing.py b/pypreprocess/reporting/check_preprocessing.py
@@ -2,7 +2,7 @@
 :Module: check_preprocessing
 :Synopsis: module for generating post-preproc plots (registration,
 segmentation, etc.)
-:Author: bertrand thirion, dohmatob elvis dopgima
+:Author: THIRION Bertrand, DOHMATOB Elvis Dopgima
 
 """
 

diff --git a/pypreprocess/reporting/preproc_reporter.py b/pypreprocess/reporting/preproc_reporter.py
@@ -1,7 +1,7 @@
 """
 :Module: reporter
 :Synopsis: utility module for report generation business
-:Author: dohmatob elvis dopgima
+:Author: DOHMATOB Elvis Dopgima
 
 """
 

diff --git a/pypreprocess/reslice.py b/pypreprocess/reslice.py
@@ -2,7 +2,7 @@
 :Module: spm_reslice
 :Synopsis: Routine functions for reslicing volumes after affine registration
 (as in motion correction, coregistration, etc)
-:Author: DOHMATOB Elvis Dopgima
+:Author: DOHMATOB Elvis Dopgimap <[email protected]>
 
 """
 

diff --git a/pypreprocess/slice_timing.py b/pypreprocess/slice_timing.py
@@ -1,7 +1,6 @@
 """
-:module: st
-:synopsis: module for STC (Slice-Timing Correction) in fMRI data
-:author: elvis[dot]dohmatob[at]inria[dot]fr
+:Synopsis: module for STC (Slice-Timing Correction) in fMRI data
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 """
 

diff --git a/pypreprocess/subject_data.py b/pypreprocess/subject_data.py
@@ -1,11 +1,11 @@
 """
-Encapsulation of subject data. Handles subject data logic
+:Synopsis: Encapsulation of subject data. Handles subject data logic
 like filetypes, extensions, .nii.gz -> .nii conversions, setup and
 teardown for reports, etc., general sanitization, etc. Also handles
 progressive report generation for subject during preprocessing.
+:Author: DOHMATOB Elvis Dopgima <[email protected]>
 
 """
-# Author: DOHMATOB Elvis Dopgima
 
 import os
 import time

diff --git a/pypreprocess/tests/test_configure_spm.py b/pypreprocess/tests/test_configure_spm.py
@@ -2,7 +2,8 @@
 """
 Created on Thu Aug  6 10:01:12 2015
 
-@author: Mehdi RAHIM, Jerome DOCKES
+:Synopsis: Checks SPM configuration
+:Author: RAHIM Mehdi, DOCKES Jerome
 """
 import os
 import stat

diff --git a/pypreprocess/time_diff.py b/pypreprocess/time_diff.py
@@ -1,17 +1,18 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-''' Time series diagnostics
-
+"""
+:Synopsis: Time series diagnostics
 These started life as ``tsdiffana.m`` - see
 http://imaging.mrc-cbu.cam.ac.uk/imaging/DataDiagnostics
 
-Oliver Josephs (FIL) gave Matthew Brett the idea of time-point to time-point
+:Author: Oliver Josephs (FIL) gave Matthew Brett the idea of time-point to time-point
 subtraction as a diagnostic for motion and other sudden image changes.
 This has been implemented in the Nipy package.
 
-We give here a simpler implementation with modified dependences
+We give here a simpler implementation with modified dependencies
+
+"""
 
-'''
 import numpy as np
 import nibabel as nib
 from nilearn.plotting import plot_stat_map

diff --git a/scripts/abide_preproc.py b/scripts/abide_preproc.py
@@ -1,7 +1,7 @@
 """
 :Module: nipype_preproc_spm_abide
 :Synopsis: SPM use-case for preprocessing ABIDE rest dataset
-:Author: dohmatob elvis dopgima
+:Author: DOHMATOB Elvis Dopgima
 
 """
 

diff --git a/scripts/hcp_preproc_and_analysis.py b/scripts/hcp_preproc_and_analysis.py
@@ -1,6 +1,6 @@
 """
 :Synopsis: preprocessing and/or analysis of HCP task fMRI data
-:Author: DOHMATOB Elvis Dopgima <[email protected]> <[email protected]>
+:Author: DOHMATOB Elvis Dopgima
 
 """
 

diff --git a/spike/glm_utils.py b/spike/glm_utils.py
@@ -9,9 +9,9 @@
 one-to-one mapping a subset of bold files, unto onset / timing
 files.
 
+:Author: DOHMATOB Elvis Dopgima
 
 """
-# Author: Elvis DOHMATOB, Christophe PALIER
 
 import os
 import glob