Denis Schluppeck schluppeck

Here are some hints

Denis Schluppeck, 2025-03-20, help for DAFNI students

... on how to get from coordinates reported in MM (often with negative numbers, because images are centered on 0,0,0) to VOXEL coordinates in SPM.

The matlab script test_coords.m included below shows you how you can go about this. It should work with minor modifications. See also comment on this gist for where in SPM you can find info about locations of voxels.

Some assorted one-liners in #rstats, #zsh, etc

work in progress.

Copy / paste data from #rstats

# assuming a table of eg student data in a dataframe D

library(clipr)

Leverage libreoffice to do this job.

Might have to install libreoffice - on macos using brew one way to do this is:

brew install  libreoffice-language-pack --cask libreoffice`

Key idea: use soffice `--headless`

Data and spreadsheet

The 2nd year lab for the Psychology and Cognitive Neuroscience course (University of Nottingham) walks students through the main ideas behind the use of linear regression in the analysis of functional magnetic resonance imagingn (fMRI) data.

The instructor provides three selected, indicative timeseries samples from a 4d data set.

The data were acquired in a standard faces versus objects, category localiser experiment. For details, [see this FAQ document](https://schluppeck.github.io/PCN-Y2-questions/#what-were-the-stimuli

Data files:

Conversion notes

Denis Schluppeck, 2023-07-21

Converting GE data via XNAT at SPMIC/Psychology. Trying to find a consistent workflow for Psychology users, especially for fMRI and related.

things to consider

voxel sizes 2mm isotropic to 2.5mm or even 3mm? SNR gains, data size
dummies. GE protocol includes data even before steady-state is reached. Therefore need to cut this by hand? Principled way of doing this in pre-processing in mrTools?

script example from PSGY4009 / lecture 6

denis schluppeck, 2022-11-07

Make sure you have access to data. I used the following dataset / files for the demos here:

https://github.com/schluppeck/hands-on-brain-data

Download the data (click the green button, download ZIP, unzip). Or if you know how to use git/github, you can also clone the repo

situation

need to quickly find out which packages a set of julia files are using. in my case, this was to create an environment after the fact... so I can ship it to people who have a clean install.

quick hack: grep through .jl files and find bits of text that start with "using"

not perfect, but got me 90% of the way there

grep "^\W*using" *.jl | cut -d: -f2 | sed s/using// | tr -d "[:blank:]" | sort | uniq

some ideas for looping over dirs, files w/ `bash`

setup some folders and files

need to have files and folders to play with. here all size 0 files, adapt to your own needs...

# create a directory and go there
cd ~

	### A Pluto.jl notebook ###
	# v0.19.40

	using Markdown
	using InteractiveUtils

	# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
	macro bind(def, element)
	quote
	local iv = try Base.loaded_modules[Base.PkgId(Base.UUID("6e696c72-6542-2067-7265-42206c756150"), "AbstractPlutoDingetjes")].Bonds.initial_value catch; b -> missing; end

	%% example of tiled plots with shared axes and labels
	%
	% ds 2022-07-22

	figure()

	nRows = 4;
	nCols = 4;
	t = tiledlayout(nRows,nCols,'TileSpacing','Compact');