https://github.com/vsoch/TtoZ

Convert T score brain statistical map to Z score map
https://github.com/vsoch/TtoZ

Last synced: 1 day ago
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Convert T score brain statistical map to Z score map

• Host: GitHub
• URL: https://github.com/vsoch/TtoZ
• Owner: vsoch
• License: mit
• Created: 2015-03-14T19:47:51.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2024-01-25T14:21:15.000Z (10 months ago)
• Last Synced: 2024-11-07T12:54:32.518Z (6 days ago)
• Language: Python
• Size: 4.29 MB
• Stars: 17
• Watchers: 3
• Forks: 8
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# TtoZ

[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.32508.svg)](http://dx.doi.org/10.5281/zenodo.32508)

TtoZ is a python implementation of Hughett's t-to-z tranform for whole brain statistical maps. 

For background about the problem, see [Hughett's paper](doc/JStats_Hughett.pdf). For a detailed example of the problem pertaining to whole brain statistical maps, see [this ipython notebook](http://nbviewer.ipython.org/github/vsoch/TtoZ/blob/master/doc/t_to_z_procedure.ipynb). For a more concise summary of the particular problems addressed by Hughett's algorithm, as compared to traditional procedures using scipy see [this ipython notebook](http://nbviewer.ipython.org/github/vsoch/TtoZ/blob/master/doc/TtoZ_method_comparison.ipynb).

[![distributions](doc/histograms.png)](https://raw.githubusercontent.com/vsoch/TtoZ/master/doc/histograms.png)  

Here we show the image histograms (from mricron) for: 

 1. [the original t-stat map](example/tfMRI_LANGUAGE_STORY.nii_tstat1.nii.gz) with 484 degrees of freedom, 

 2. a [z-score map](example/zstat_afni.nii) produced with AFNI's 3dcalc (`3dcalc -a tstat.nii.gz -expr 'fitt_t2z (a,484)' -prefix afni_zstat.nii -float`), 

 3. a [z-score map](example/zstat_nosplit.nii) [our original effort](http://nbviewer.ipython.org/github/vsoch/TtoZ/blob/master/doc/t_to_z_procedure.ipynb#Converting-from-P-Values-to-Z-Scores) using scipy.stats that did not split into +/- values, and 

 4. a [z-score map](example/zstat_ttz.nii) produced with TtoZ (Hughett's method that splits at 0 into two sets first). 

2) and 3) have truncation of the distributions.  For both 3) and 4) it was also necessary to convert p-values exactly == 1 to 0.999999, as a value of exactly 1 will be converted to inf when converted to the standard normal score.

Note that the y-axis scales are slightly different, most noticably for the second image, 3dcalc, which extends to a density of 2.0 due to the number of zeros that are replaced to prevent error. 

# Installation

     pip install git+https://github.com/vsoch/TtoZ.git

or from pypi:

    pip install TtoZ

# Usage

      usage: TtoZ [-h] --t_stat_map T_STAT_MAP --dof DOF [--output_nii OUTPUT_NII]

      Convert a whole brain T score map to a Z score map without loss of precision

      for strongly positive and negative values.

      optional arguments:

       -h, --help            show this help message and exit

        --t_stat_map T_STAT_MAP

                              T-score statistical map in the form of a 3D NIFTI file

                              (.nii or .nii.gz).

        --dof DOF             Degrees of freedom (eg. for a two-sample T-test:

                              number of subjects in group - 2)

        --output_nii OUTPUT_NII

                              The name for the output Z-Score Map.

# Example

     TtoZ --t_stat_map=t_stat_map.nii.gz --dof=484 --output_nii=z_score_map.nii