pip install git+https://github.com/chrisfilo/alleninf.git

usage: scripts.py [-h] [--inference_method INFERENCE_METHOD]
                  [--n_samples N_SAMPLES] [--n_burnin N_BURNIN]
                  [--probes_reduction_method PROBES_REDUCTION_METHOD]
                  [--mask MASK] [--radius RADIUS]
                  [--probe_exclusion_keyword PROBE_EXCLUSION_KEYWORD]
                  stat_map gene_name

Compare a statistical map with gene expression patterns from Allen Human Brain
Atlas.

positional arguments:
  stat_map              Unthresholded statistical map in the form of a 3D
                        NIFTI file (.nii or .nii.gz) in MNI space.
  gene_name             Name of the gene you want to compare your map with.
                        For list of all available genes see: http://help.brain-map.org/download/attachments/2818165/HBA_ISH_GeneList.pdf?version=1&modificationDate=1348783035873.

optional arguments:
  -h, --help            show this help message and exit
  --inference_method INFERENCE_METHOD
                        Which model to use: fixed - fixed effects,
                        approximate_random - approximate random effects
                        (default), bayesian_random - Bayesian hierarchical
                        model (requires PyMC3).
  --n_samples N_SAMPLES
                        (Bayesian hierarchical model) Number of samples for
                        MCMC model estimation (default 2000).
  --n_burnin N_BURNIN   (Bayesian hierarchical model) How many of the first
                        samples to discard (default 500).
  --probes_reduction_method PROBES_REDUCTION_METHOD
                        How to combine multiple probes: average (default) or
                        pca - use first principal component (requires scikit-
                        learn).
  --mask MASK           Explicit mask for the analysis in the form of a 3D
                        NIFTI file (.nii or .nii.gz) in the same space and
                        dimensionality as the stat_map. If not specified an
                        implicit mask (non zero and non NaN voxels) will be
                        used.
  --radius RADIUS       Radius in mm of of the sphere used to average
                        statistical values at the location of each probe
                        (default: 4mm).
  --probe_exclusion_keyword PROBE_EXCLUSION_KEYWORD
                        If the probe name includes this string the probe will
                        not be used.

$ alleninf SetA-SetB_Tstat.nii.gz HTR1A --mask SetA_mean.nii.gz

Fetching probe ids for gene HTR1A
Found 3 probes: A_24_P97687, CUST_575_PI417557136, CUST_15880_PI416261804
Fetching expression values for probes A_24_P97687, CUST_575_PI417557136, CUST_15880_PI416261804
Found data from 3702 wells sampled across 6 donors
Combining information from selected probes
Translating locations of the wells to MNI space
Checking values of the provided NIFTI file at well locations
70 wells fall outside of the mask
Performing approximate random effect analysis
Correlation between NIFTI values and HTR1A expression averaged across donors = -0.372743 (t=-12.8453, p=5.0909e-05)