TopicSPM
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…
- Analysis Threshold Masking in SPM
By default, SPM masks the images that contribute to an analysis at the Estimation stage. If a voxel is masked out because it fails to exceed an arbitrary analysis threshold (set to a defulat of 0.8…
- Making SPM faster
Here's an interesting wikibooks page detailing how you can make SPM faster. Some of the tweaks involve simply adjusting the spm_defaults.m to utilise the amount of RAM you have installed at the model estimation stage. Others…
- Marsbar script: Save spheres as both .img and .mat files
Below (indented) is a straightforward MATLAB/SPM/Marsbar script for generating separate Marsbar ROI and Nifti ROI spheres (user-defined radius) from a set of user-defined MNI coordinates stored in a text file ('spherelist.txt' saved in the same directory…
2011
- SPM: Changing the default number of tabulated local maxima
SPM will, by default, show you 3 local maxima within each cluster displayed when you click 'whole brain' within Results. To change the default number of local maxima displayed in the output table, edit spm_list.m and…
- 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
- Marsbar error in pr_stat_compute
Do not duplicate I ran into the following error when trying to use a script to make Marsbar extract betas Error in pr_stat_compute at 34 Indices too large for contrast structure This problem occurred when I…
- 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…