[REL] version 3.0.0 (#886)

* bump version and make release

* fix spelling

Author: Remi-Gau

CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 
 title: "bidspm"
 
-version: 2.3.0
+version: 3.0.0
 
 abstract: bidspm is a set of pipelines and tools for Octave / MATLAB to process and analyze BIDS data sets using SPM12.
 

Dockerfile

@@ -10,7 +10,7 @@ USER root
 ENV LANG="en_US.UTF-8" \
     LC_ALL="en_US.UTF-8"
 
-LABEL version="2.3.0"
+LABEL version="3.0.0"
 
 LABEL maintainer="Rémi Gau <[email protected]>"
 
@@ -54,11 +54,11 @@ WORKDIR /home/neuro
 RUN mkdir code input output
 
 # uncomment when local development
-RUN echo '\nDEV'
-COPY . /home/neuro/bidspm
+# RUN echo '\nDEV'
+# COPY . /home/neuro/bidspm
 
-# RUN echo '\nPROD'
-# RUN git clone --depth 1 --branch FIXME --recursive https://github.com/cpp-lln-lab/bidspm.git
+RUN echo '\nPROD'
+RUN git clone --depth 1 --branch FIXME --recursive https://github.com/cpp-lln-lab/bidspm.git
 
 RUN cd bidspm && make install
 

README.md

@@ -11,7 +11,7 @@
   [![GitHub last commit](https://img.shields.io/github/last-commit/cpp-lln-lab/bidspm)](https://github.com/cpp-lln-lab/bidspm.git)
   [![All Contributors](https://img.shields.io/badge/all_contributors-14-orange.svg?style=flat-square)](https://github.com/cpp-lln-lab/bidspm#contributors)
 
-<!-- [![HitCount](https://hits.dwyl.com/cpp-lln-lab/bidspm.svg?style=flat-square&show=unique)](http://hits.dwyl.com/cpp-lln-lab/bidspm) -->
+<!--  [![HitCount](https://hits.dwyl.com/cpp-lln-lab/bidspm.svg?style=flat-square&show=unique)](http://hits.dwyl.com/cpp-lln-lab/bidspm) -->
 
 
 # bidspm
@@ -218,7 +218,7 @@ Please see our
   license = {GPL-3.0},
   title   = {bidspm},
   url = {https://github.com/cpp-lln-lab/bidspm},
-  version = {2.3.0}
+  version = {3.0.0}
   doi     = {10.5281/zenodo.3554331},
   publisher = {Zenodo},
   journal = {Software}

docs/bidspm-manual.pdf

@@ -33,8 +33,10 @@
 opt.dir.output = ''  ;
 opt.dir.preproc = ''  ;
 opt.dir.raw = ''  ;
+opt.dir.roi = 'derivatives/bidspm-roi'  ;
 opt.dir.stats = ''  ;
 opt.dryRun = 0, ;
+opt.dummy_scans = 0.000, ;
 opt.funcVolToSelect = []  ;
 opt.funcVoxelDims = []  ;
 opt.fwhm.contrast = 0.000, ;

docs/source/default_options.m

@@ -206,6 +206,10 @@ batches preproc
 
 IO
 ==
+.. _addGitIgnore:
+.. autofunction:: src.IO.addGitIgnore
+.. _addReadme:
+.. autofunction:: src.IO.addReadme
 .. _cleanCrash:
 .. autofunction:: src.IO.cleanCrash
 .. _createDerivativeDir:
@@ -392,6 +396,8 @@ infra
 .. autofunction:: src.infra.returnRtdURL
 .. _setGraphicWindow:
 .. autofunction:: src.infra.setGraphicWindow
+.. _silenceOctaveWarning:
+.. autofunction:: src.infra.silenceOctaveWarning
 
 
 .. _messages:
@@ -564,10 +570,14 @@ stats utils
 .. autofunction:: src.stats.utils.createGlmDirName
 .. _designMatrixFigureName:
 .. autofunction:: src.stats.utils.designMatrixFigureName
+.. _fillInResultStructure:
+.. autofunction:: src.stats.utils.fillInResultStructure
 .. _getContrastNb:
 .. autofunction:: src.stats.utils.getContrastNb
 .. _getRegressorIdx:
 .. autofunction:: src.stats.utils.getRegressorIdx
+.. _isTtest:
+.. autofunction:: src.stats.utils.isTtest
 .. _labelActivations:
 .. autofunction:: src.stats.utils.labelActivations
 .. _returnContrastImageFile:
@@ -594,8 +604,6 @@ utils
 .. autofunction:: src.utils.getDist2surf
 .. _getFuncVoxelDims:
 .. autofunction:: src.utils.getFuncVoxelDims
-.. _isTtest:
-.. autofunction:: src.utils.isTtest
 .. _isZipped:
 .. autofunction:: src.utils.isZipped
 .. _regexify:

docs/source/dev_doc.rst

@@ -3,7 +3,7 @@ @software{bidspm
   license   = {GPL-3.0},
   title     = {bidspm},
   url       = {https://github.com/cpp-lln-lab/bidspm},
-  version   = {2.3.0}
+  version   = {3.0.0}
   doi       = {10.5281/zenodo.3554331},
   publisher = {Zenodo},
   journal   = {Software}

docs/source/examples/bidspm.bib

@@ -1,24 +1,22 @@
 ## Pre processing
 
-The (f)MRI data were pre-processed with bidspm (v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
+The (f)MRI data were pre-processed with bidspm (v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
 using statistical parametric mapping
 (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
 https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
 using MATLAB 9.4.0.813654 (R2018a)
-on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
+on a unix computer (Linux version 5.15.0-56-generic (build@lcy02-amd64-004) (gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022
 )
 .
 
 
 The preprocessing of the functional images was performed in the following order:
-- removing of dummy scans
 - slice timing correction
 - realignment and unwarping
 - segmentation and skullstripping
 - normalization MNI space
 - smoothing
 
-{{nb}} dummy scans were removed to allow for signal stabilization.
 
 Slice timing correction was performed
 taking the ^th slice as a reference
@@ -58,5 +56,5 @@ gaussian kernel (FWHM = 6 mm).
 ## References
 
 This method section was automatically generated using bidspm
-(v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
+(v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
 and octache (https://github.com/Remi-Gau/Octache).

docs/source/examples/preprocess_citation.md

@@ -1,11 +1,11 @@
 ## fMRI statistical analysis
 
-The fMRI data were analysed with bidspm (v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
+The fMRI data were analysed with bidspm (v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331 - [@bidspm])
 using statistical parametric mapping
 (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
 https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
 using MATLAB 9.4.0.813654 (R2018a)
-on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
+on a unix computer (Linux version 5.15.0-56-generic (build@lcy02-amd64-004) (gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022
 )
 
 The input data were the preprocessed BOLD images in IXI549Space space for the task " facerepetition ".
@@ -43,5 +43,5 @@ to account for residual motion artefacts,
  ## References
 
 This method section was automatically generated using bidspm
-(v2.3.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
+(v3.0.0; https://github.com/cpp-lln-lab/bidspm; DOI: https://doi.org/10.5281/zenodo.3554331)
 and octache (https://github.com/Remi-Gau/Octache).