Stand alone layer fMRI software that does not rely on other fMRI software packages with its own nii reader
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LN_3DGROW_LAYERS.cpp without GSL fit dependense Sep 2, 2018
LN_BOCO.cpp fixed Gfactor bug Dec 10, 2018
LN_COLUMNAR_DIST.cpp new smoothing algorithms included Nov 3, 2018
LN_CORREL2FILES.cpp without GSL fit dependense Sep 2, 2018
LN_DEBUGGING.cpp without GSL fit dependense Sep 2, 2018
LN_DIRECT_SMOOTH.cpp new smoothing algorithms included Nov 3, 2018
LN_EXTREMETR.cpp without GSL fit dependense Sep 2, 2018
LN_FAsim.cpp without GSL fit dependense Sep 2, 2018
LN_FIX_RIM.cpp without GSL fit dependense Sep 2, 2018
LN_FLOAT_ME.cpp without GSL fit dependense Sep 2, 2018
LN_GFACTOR.cpp fixed Gfactor bug Dec 10, 2018
LN_GRADSMOOTH.cpp new smoothing algorithms included Nov 3, 2018
LN_GROW_LAYERS.cpp new smoothing algorithms included Nov 3, 2018
LN_IMAGIRO.cpp with LN_COLUMNAR_DIST Sep 26, 2018
LN_LAYER_SMOOTH.cpp new smoothing algorithms included Nov 3, 2018
LN_LEAKY_LAYERS.cpp without GSL fit dependense Sep 2, 2018
LN_NOISEME.cpp without GSL fit dependense Sep 2, 2018
LN_RAGRUG.cpp without GSL fit dependense Sep 2, 2018
LN_SHORT_ME.cpp without GSL fit dependense Sep 2, 2018
LN_SKEW.cpp with latest qiuality controll programs Nov 27, 2018
LN_SMOOTH_RIM.cpp without GSL fit dependense Sep 2, 2018
LN_SNR_int_corr.cpp without GSL fit dependense Sep 2, 2018
LN_TRIAL.cpp without GSL fit dependense Sep 2, 2018
LN_ZOOM.cpp without GSL fit dependense Sep 2, 2018
Makefile with latest qiuality controll programs Nov 27, 2018
My_nii_read.cpp without GSL fit dependense Sep 2, 2018
README.rst layout Sep 2, 2018
nifti1.h test Apr 24, 2018
nifti1_io.cpp test Apr 24, 2018
nifti1_io.h test Apr 24, 2018
nifti2.h test Apr 24, 2018
nifti2_io.cpp with Rag Rug Jul 2, 2018
nifti2_io.h test Apr 24, 2018
nifti_tool.cpp test Apr 24, 2018
nifti_tool.h test Apr 24, 2018
nifticdf.cpp test Apr 24, 2018
nifticdf.h test Apr 24, 2018
znzlib.cpp test Apr 24, 2018
znzlib.h test Apr 24, 2018

README.rst

Tutorials on layering, layer-smoothing, columnar anlysis here: https://layerfmri.com/category/code/

example image with layers and columns

This is set of standalone layer-fMRI C++ programs that do not have any other dependencies.

Bob Cox and Rick Reynolds wrote few a nii I/O that I recommend. The original version is in the AFNI sources. I collected all the necessary files and adapted them for my taste. All the necessary files are:

nifti1_io.cpp
nifti2.h
nifti2_io.h
nifti_tool.h
nifticdf.h
znzlib.h
nifti1.h
nifti1_io.h
nifti2_io.cpp
nifti_tool.cpp
nifticdf.cpp
znzlib.cpp

Using linking those allows you to use nii_datatype and load nii files in your own C++ program with the function

nifti_image * nim=NULL; nim = nifti_image_read(filename, 1);

Example

My_nii_read.cpp

It reads in a nii file, accesses the data, manipulates the individual voxels writes out the manipulated data as nii

Usage of My_nii_read.cpp 1.) download the all the files with from github E.g. with the command:

git clone https://github.com/layerfMRI/laynii

2.) go into subfolder:

cd laynii

3.) compile it with:

make all

4.) execute it with:

./My_nii_read -input input_example.nii -output output.nii -cutoff 3

For more information see: https://layerfmri.com/2017/11/30/using-a-standalone-nii-i-o-in-c/

Comment on GSL

Parts of LAYNII depend on GSL.

It seems that GSL does not have the fit option automatically included. If there is an error when compiling about gsl/gsl_fit, consider installing the dev-package: sudo apt-get install libgsl0-dev

Update 180902: The fit include has been removed.