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HIPSTA

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    HipstaPipeline
    
    __init__
    
    A more detailed description:
    
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Hipsta

`HipstaPipeline`

`init`

Hippocampal Shape and Thickness Analysis (HIPSTA) pipeline.

Parameters:

Name	Type	Description	Default
`subject`	`BIDSSubject`	A BIDS subject object.	required
`session`	`BIDSSession`	A BIDS session object.	required
`output_path`	`str`	Output directory to save results.	required
`use_freesurfer_clinical`	`bool`	Whether to use recon-all-clinical.sh outputs. Default is False.	`False`

A more detailed description:

Installation

pip install hipsta

Other considerations:

only gmsh version 2.x is supported (do not use gmsh 4.x or later).

cd ~
wget https://gmsh.info/bin/Linux/gmsh-2.16.0-Linux64.tgz

tar -xzf gmsh-2.16.0-Linux64.tgz

echo 'export PATH=$HOME/gmsh-2.16.0-Linux/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

Newer versions of scipy may cause issues: ValueError: all the input arrays must have same number of dimensions, but the array at index 0 has 1 dimension(s) and the array at index 1 has 0 dimension(s). A python script to fix this issue is provided in <cvdproc>/pipelines/smri/hipsta/patch_hipsta_mode.py.