For questions about methodology and tools related to functional magnetic resonance imaging. For general questions about brain-structure use neurobiology, and for general imaging questions use neuroimaging.

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Generate fMRI from neurotransmitter consumption

As mentioned in this answer, it's possible to generate an fMRI BOLD signal from neurotransmitter consumption. What equation would be appropriate for this use?
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How are abstract relations represented neurally?

It is known that concepts with similar attributes (color, shape... Etc.) are represented in a similar manner in the brain. However, is there any evidence of abstract relations, such as the as causal ...
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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 ...
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(Co)Registration in the preprocessing pipeline

I have a general question about registration and coregistration in the preprocessing pipeline of fMRI images. For me it is not clear what this is. So, motion correction, slice time correction, ...
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What does O- mean in a NIFTI file name of an MRI?

I am exploring brain MRI scans. Using MRIConvert, I converted dcm files to NIFTI. Some of the outputted NIFTI files have O- in their filenames and I could not figure out what does it mean. Example ...
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How to display Talairach Image in AFNI correctly?

I am using AFNI to display Talairach image, that is anat+tlrc.BRIK & anat+tlrc.HEAD . But the AFNI only shows part of the image. It looks like this: AFNI is ...
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Brain extraction and save images as .img file

I have been working on Auditory data (from FIL) to read the .img files as numeric numbers of intensity of each voxels over time in array/matrix format using AnalyzeFMRI package in R. It gives me ...
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How to read ROI location from .nii file?

NIFTI file formats (.nii) are used to store MRI/fMRI data in. I have a NIFTI file that is supposed to contain the locations of 375 brain regions. I am having trouble working with the file (it was ...
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Independent Component Analysis (ICA) in FSL vs fastICA: Why do they vary?

I was doing ICA in FSL via Melodic gui and fastICA in R on Auditory data from SPM http://www.fil.ion.ucl.ac.uk/spm/data/auditory/. No matter whether I keep the default settings in Melodic gui or ...
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Descriptions of functions of brain areas listed in the Harvard Oxford Atlas

I am interested in finding a resource describing the functions of the areas listed in the Harvard Oxford Atlas of the human brain. It would be considered a bonus if it were machine readable (e.g. ...