Computational protocol: Functional Anatomy of the Masking Level Difference, an fMRI Study

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Protocol publication

[…] Dicom image files were converted to NIfTI format using dcm2nii (MRIcron; http://www.sph.sc.edu/comd/rorden/mricron/). Realignment and co-registration of functional images to the participants T1 weighted image was performed using SPM5 (http://www.fil.ion.ucl.ac.uk/spm). Segmentation was performed on the participant's T1 image, which provided spatial normalization parameters for transforming the co-registered functional images into the coordinate system of the provided SPM templates. Scans were smoothed using an 8×8×8 mm Gaussian kernel. After using SPM5 to create the general linear model including all conditions for each session, SPMd was used to identify outlying scans. Next, a first -level SPM analysis was then performed for each subject which included all four sessions, but excluded scans identified by SPMd as having greater than 30 times the median number of outlier voxels, or which had more than 1 mm total motion from the previous scan. The first-level analysis provides separate images showing activation for each individual for each contrast. A second-level analysis was then performed using the contrast images produced for each individual in order to make statistical parametric maps. […]

Pipeline specifications

Software tools MRIcron, SPM
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Diseases, Leukodystrophy, Metachromatic, Masked Hypertension