Miscellaneous scripts for analysis of structural MRI data

get_euler_qa.py

Get average euler number from freesurfer directory. A measure of image quality. Works on python 3.7.6

hp_ant_post_wmhypo.sh

A script for measuring the anterior-posterior distribution of the freesurfer white matter hypointensity label. I used to it to measure the distribution of heterotopic GM nodules in people with periventricular nodular heterotopia, providing quantitative evidence that these nodules are mainly posterior (see http://www.sciencedirect.com/science/article/pii/S0920121114002897/). This is set up to run on my computer which runs the version of FSL provided by neurodebian, so fsl commands are all prefixed with "fsl5.0-"

load.mgh.R

loads Freesurfer mgh files into R

save.mgh.R

saves mgh files from R

read.label.R

read Freesurfer label files into R

vertex.wise.equivalence.R

carry out vertex-wise equivalence testing analyses on Freesurfer-derived morphometric estimates. See https://sites.google.com/site/hpardoe/equivalence for instructions and https://peerj.com/preprints/808v1/ for a paper about it.

adni.xml.reader.R

turn list of adni xml files into R data frame. Put xml files in directory called "xml" under your working directory, then in R: my.df <- xml.list.to.df(xml.file.list)

hcp_scan_download.sh

download scans for human connectome project. Replace "/home/hpardoe/Dropbox/human.connectome/s3cfg" with location of your own s3cfg file