TopicfMRI
2010
- Masking in SPM5
Masking is an extremely useful function within SPM. For example, you might want to see whether your parietal cue-related activation is subsumed by, or independent of, the parietal retrieval-success activation that is reliably found in the…
- Whole Brain Mask
Whole brain masks are produced by SPM when estimating a model. They're great to look over if you want to check the extent of participant movement (a quick heuristic is to examine whether movement has been…
- Understanding what SPM does to establish significant 'activations'
I recently came across a web-page I should have committed to memory years ago, when I was first starting to get to grips with SPM analysis: Matthew Brett's Introduction to SPM Statistics It's a fantastically straightforward…
- Keeping residuals after SPM estimation
Occasionally, it's nice to look under the bonnet and see what's going on during any automated process that you take for granted. More often than not, I do this when the automaticity has broken down and…
- Not-so-restful resting connectivity fMRI (pt.1)
Last week, during a very interesting Brain, Behavior and Cognition colloquium given by Steve Nelson , Jeff Zacks asked a thought-provoking question. He wanted to know what fMRI connectivity maps would look like if you performed…
- Not-so-restful resting connectivity fMRI (pt.2)
Things I have (re-)learned this week: - Conducting resting connectivity analyses on 60mins worth of 2s TR fMRI data from 19 participants takes time; - It is always a good idea to do a quick literature…
- What a Relief!
1 commentfMRI
fMRI studies, which measure blood oxygenation-dependent (BOLD) signal, do report brain activations. It seems obvious, but it's been subject to debate. Why? - well, largely because validations of the technique have tended to involve stimulating neurons…
- The 80% Rule of fMRI Participants
Only 80% of scheduled participants produce datasets where data from all runs is usable. That's the conclusion I have drawn from my limited experience of scanning participants for research here at Washington University. My running totals…
- The Physical Reality of fMRI Slice Acquisition Order
Typical fMRI brain scans take a 3D images of the head every few seconds. These images are composed of lots of 2D 'slices' (usually axially oriented) stacked on top of one another. This is where the…
- Backing up fMRI data manually
Whilst Windows easily copies lots of data, it struggles when you ask it to copy lots and lots and lots of data. Teracopy is a neat file copying utility that provides peace of mind as you…
2011
- Call for PhD Applications
2 commentsfMRI
Out with the old, in with the new: Novelty judgements as a translational tool to assess healthy ageing Funding Notes: The student will require a minimum of an upper second class Hons Degree and is open…
- SPM: DICOM Import Error
Since setting up lab in St Andrews I've consistently run into a DICOM Import Error that causes the process to terminate about half-way through. I finally fixed the problem today after a quick search on the…
2012
- Converting 3D nifti images to a 4D image with SPM
The past few days have seen my fMRI analysis server taken over by a Linux virtual machine. I have installed FSL , and have been using MELODIC to plough my way through ICA analyses of fcMRI…
- Brain Outlines
Below are some quick-and-dirty brain outline images I'm using in a talk I'm giving in a couple of weeks. I like the calligraphic quality that the axial and sagittal slices have. The coronal image is a…
2013
- Twitter on MVPA
I often bang on about how useful twitter is for crowd-sourcing a research community. Today I was reminded of quite brilliant the people on twitter can be at helping to overcome an 'I don't know where…
2016
- This is your brain on... déjà vu
At the International Conference on Memory last month, I presented some new work from my lab, a 21 participant, fMRI-scanned, memory experiment. We imaged people's brains as they underwent a procedure that generates sensations likened to…