digressions on (mouse) brain imaging

 

Understanding data tree using a toy example

RMINC
data tree
How to work with and manipulate data trees, such as the RMINC hierarchical anatomy tree
Aug 5, 2025
Linh Pham

 

RMINC tips when working with many files

RMINC
BMRC
longitudinal
high-throughput
Tips for using RMINC when you have many images to parse through.
Jul 30, 2025
Linh Pham

Under the hood: visualizations in RMINC

RMINC
How RMINC projects and visualizes results using a sample cross-sectional comparison.
Jul 30, 2025
Linh Pham and Jason Lerch

 

Annotated pyro5 command

pydpiper
Oxford
longitudinal
How to run PydPiper using the Pyro5 backend, as demonstrated by the Tamarack pipeline
Jul 29, 2025
Linh Pham

 

Mounting cluster filesystems on your mac

mac
Using SSHFS to get read/write access to cluster filesystems
Jul 27, 2025
Jason Lerch

 

MINC tools on a new mac

RMINC
mac
How to install MINC, RMINC, etc. on a new mac
Jul 24, 2025
Jason Lerch

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 …
Aug 29, 2023
Jason Lerch
No matching items