MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. MRIcro is a small program that runs on Apple OSX for viewing the NIfTI format of medical images popular with scientists (medical DICOM images can be converted to NIfTI using tools like my free dcm2nii).
Thresholding the results
Results from the corresponding model can be thresholded to a given uncorrected or corrected statistical significance level, obtaining peak coordinates, clusters breakdowns and NIfTI images. This will also open MRIcron brain viewer to display the results (if MRIcron is enabled; see Settings section for help on setting up MRIcron integration).
Please find citation information for the atlas by Catani, Thiebautde Schotten et al below.
One-tailed vs two-tailed
As in most neuroimaging software, this dialog conducts a pair of one-tailed tests. To avoid doubling the false positive rate, please halve the statistical significance level (e.g., to 0.025).
To threshold a map
Press the button [Threshold]
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or:
Select [Threshold] in the Statistics menu, to open the following dialog:
Command-line and batch usage
thresholdp_map_path,z_map_path,value,minimum number of voxels
Example:
threshold analysis_MyMean/corrp_tfce,analysis_MyMean/MyMean_z,0.05,10
Note: p-map and z-map paths should NOT include the extension .nii.gz
References
(effect-sizes and variances):Radua J, Mataix-Cols D, Phillips ML, El-Hage W, Kronhaus DM, Cardoner N andSurguladze S. A new meta-analytic method for neuroimaging studies that combinesreported peak coordinates and statistical parametric maps.Eur Psychiatry 2012; 27:605–611..
(white matter atlas 1):Thiebaut de Schotten M, Dell'Acqua F, Forkel SJ, Simmons A, Vergani F,Murphy DG and Catani M. A lateralized brain network for visuospatialattention.Nat Neurosci 2011; 14:1245-1246..
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(white matter atlas 2):Thiebaut de Schotten M, Ffytche DH, Bizzi A, Dell'Acqua F, Allin M,Walshe M, Murray R, Williams SC, Murphy DG and Catani M.Atlasing location, asymmetry and inter-subject variability of whitematter tracts in the human brain with MR diffusion tractography.Neuroimage 2011; 54:49-59..
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(white matter atlas 3):Rojkova K, Volle E, Urbanski M, Humbert F, Dell'Acqua F andThiebaut de Schotten M. Atlasing the frontal lobe connections and theirvariability due to age and education: a spherical deconvolutiontractography study.Brain Struct Funct 2015; in Press..