digressions on (mouse) brain imaging

Creating a pydpiper init model

pydpiper

Steps for creating an init model from scratch

Atlas colours as plot legends

R

longitudinal

RMINC

MRIcrotome

Using colours from the atlas can make an effective way to label multiple bits on a plot

Developmental analyses, part 2

R

longitudinal

RMINC

MRIcrotome

How to deal with longitudinal brain development data, this time focusing on working across all ROIs in the brain

Developmental analyses, part 1

R

longitudinal

How to deal with longitudinal brain development data

Copying important pydpiper outputs

pydpiper

Some rsync commands to only copy important bits from a pydpiper pipeline

Better MRIcrotome brain outlines

R

MRIcrotome

RMINC

How to make better brain outlines for MRIcrotome

SCT power analyses

R

Understanding power for the SCT mouse model with some digressions into power in non-orthogonal designs

Jason Lerch and Kamila Szulc-Lerch

Annotated MBM command

pydpiper

An annotated version of a simple MBM.py command to give a sense of all those pesky options

MINC tools on BMRC cluster

Oxford

How to use the MINC tools, including RMINC in RStudio, on Oxford’s BMRC cluster

Welcome

news

Welcome to this blog, which is mostly motivated by the poor state of documentation around various mouse brain imaging analysis tools, in particular the pydpiper pipelines and …