Additive Signal Change Analysis tool

Version 0.2.0 --- 2017-12-16

[Repository][REPOSITORY] --- [Changelog][CHANGELOG] --- [License][LICENSE]

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Eugene Duff

FMRIB Centre, University of Oxford

Contact me if you are interested in running ASC.

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Dependencies

*ASC * uses Python 3 and FSL

Python dependencies are the following, to be included in [FSLpy]

Python

• NumPy: The fundamental package for scientific computing with Python.
• SciPy: A Python-based ecosystem of open-source software for mathematics, science, and engineering.
• matplotlib: A python 2D plotting library.
• Spectrum Basic spectral Analysis Tools for dof estimation. * temporary *
• MNE: visualisation tools. * temporary *
• NiBabel: Provides read / write access to some common neuroimaging file formats. * optional *

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Setup environment

>> source <ascdir>/setup.py

Usage

usage: asc.py [-h] -d DIR --inds1 INDS1 --inds2 INDS2 [-o OUT_FNAME]
              [--pcorrs PCORRS] [--errdist_perms ERRDIST_PERMS]
              [--min_corr_diff MIN_CORR_DIFF] [--prefix PREFIX] [--pctl PCTL]
              [--subj_order SUBJ_ORDER] [--exclude_conns EXCLUDE_CONNS]

FMRI Additive Signal Analysis

optional arguments:

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

required arguments:

  -d DIR, --dir DIR     dual_regression dir
  --inds1 INDS1         index file 1
  --inds2 INDS2         index file 2

optional arguments:

  -o OUT_FNAME, --out_fname OUT_FNAME
                        output file [asc.pdf]
  --pcorrs PCORRS       use partial correlation
  --errdist_perms ERRDIST_PERMS
                        permutations for monte carlo
  --min_corr_diff MIN_CORR_DIFF
                        minimum correlation change
  --prefix PREFIX       dr prefix
  --pctl PCTL           percentile of connections to show (FDR)
  --subj_order SUBJ_ORDER
                        subject_order
  --exclude_conns EXCLUDE_CONNS
                        exclude connections

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Basic Usage - Apply to Dual Regression dir

usage: asc.py -d dual_reg.dr --inds1 1,2,3,4,5,6,7,8,9,10 --inds2 10,12,13,14,15,16,17,18,19,20  -o asc_results
              --pcorrs True --errdist_perms 1500
              [--min_corr_diff MIN_CORR_DIFF] [--prefix PREFIX] [--pctl PCTL]
              [--subj_order SUBJ_ORDER] [--exclude_conns EXCLUDE_CONNS]

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[REPOSITORY]: https://git.fmrib.ox.ac.uk/eduff/ampconn/blob/release"ASC Repository [CHANGELOG]: https://git.fmrib.ox.ac.uk/eduff/ampconn/blob/release/CHANGELOG.md "ASC Changelog" [LICENSE]: https://git.fmrib.ox.ac.uk/eduff/ampconn/blob/release/LICENSE "ASC License file"

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