digressions on (mouse) brain imaging

Creating a pydpiper init model

pydpiper

Steps for creating an init model from scratch
Apr 3, 2024
Jason Lerch

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
Dec 10, 2023
Jason Lerch

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
Dec 1, 2023
Jason Lerch

Developmental analyses, part 1

R
longitudinal

How to deal with longitudinal brain development data
Nov 26, 2023
Jason Lerch

 

Copying important pydpiper outputs

pydpiper

Some rsync commands to only copy important bits from a pydpiper pipeline
Oct 19, 2023
Jason Lerch

Better MRIcrotome brain outlines

R
MRIcrotome
RMINC

How to make better brain outlines for MRIcrotome
Sep 16, 2023
Jason Lerch

SCT power analyses

R

Understanding power for the SCT mouse model with some digressions into power in non-orthogonal designs
Sep 6, 2023
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
Sep 2, 2023
Jason Lerch

MINC tools on BMRC cluster

Oxford

How to use the MINC tools, including RMINC in RStudio, on Oxford’s BMRC cluster
Aug 29, 2023
Jason Lerch

 

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 RMIN…
Aug 29, 2023
Jason Lerch
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