Questions tagged [spm]

For questions about statistical parameter mapping (SPM).

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Reproducible Dynamic Causal Modeling/ model based effective connectivity analysis for fMRI

I am doing a Masters degree in Cognitive Neuroscience and was thinking on doing my master thesis on effective connectivity in Theory of Mind. I like the model-based approach of Dynamic Causal Modeling ...
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0answers
31 views

fMRI ROI analysis: independence

In a 2x2 factorial, is it appropriate to look at an interaction at the second-level, group analysis (e.g., using SPM) and define this as an ROI to restrict follow-up main effect contrasts? Or is this ...
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33 views

Compute single patient Z-Scores from atlas anatomical zone

I have one brain image from a single patient. I have a set of normal pateints. Both, single patient and normal patients are normalised to an SPM template and the NMI space. I also have a brain atlas (...
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0answers
41 views

SPM5 - contrast vectors too long when applied to a new SPM.mat file

Background: I am using fMRI individual level analysis data from my supervisor's previous paper. Before I can perform PPI on the data, I need to update the 1st level analysis batch files since they ...
2
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1answer
31 views

“st” global variable in SPM8

I have some legacy preprocessing code that is designed to use SPM8. In the alignment function, it refers to a global variable st, which as far as I can tell is not ...
3
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1answer
65 views

What are the main differences between the FreeSurfer volumetric approach and the statistical parametric mapping from SPM?

In modern research of brain volume and function there are two main players. FreeSurfer which is free of cost and open source and the older, but more frequently used, statistical parametric mapping ...
5
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1answer
139 views

What do NaNs represent in an SPM β-map?

I've estimated a model for an fMRI dataset, so I now have a beta_*.nii file for each regressor in my model. In a seperate step, I've defined ROIs using marsbar and ...
2
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0answers
249 views

Are there any equivalence between the Desikan-Killiany atlas to brodmann areas?

FreeSurfer makes inferences about volume, through the calculation of the surface of the brain. The parametric method (used in SPM) is a voxel-based statistics. FreeSurfer analysis does not map the ...
2
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2answers
934 views

How to install MARSBAR toolbox in SPM12?

I am trying to install MARSBAR toolbox into SPM12, but I am running into different problems. Initially they were all related to directory ownership and permissions (using Ubuntu 14.04), which I ...
2
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1answer
135 views

Finding the anterior comissure to set origin in a SPECT image using SPM/ISAS

I am learning how to use SPM and ISAS to analyze ictal and interictal SPECT. However I am stuck at a point of their tutorial. In the item 1.2 one has to set the origin for the SPECT image. That is, ...
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1answer
183 views

How to import images used to analysis in SPM to FreeSurfer

FreeSurfer uses the recon-all command to semi-automatically generate its statistics. This tool implies a certain directory structure in which the files with the images for the samples should be ...
5
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1answer
1k views

Why is my SPM batch job printing a warning repeatedly?

I'm aware of the ambivalence of cogsci.stacexchange with regards to asking questions about code, but this question really is about SPM, specifically, so I think that the domain-specific nature of my ...
5
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1answer
276 views

Is there a good entry-level tutorial for SPM?

The title pretty much says it all. I need to do some fMRI data analysis and I can't find any entry-level tutorials for Statistical Parameter Mapping (SPM). I've looked at some of the videos on the ...