Computational protocol: Migraine attacks the Basal Ganglia

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Protocol publication

[…] fMRI analysis was carried out using FMRIB Software Library (FSL) (, version 4.1.3. The initial two volumes were removed from each of the functional scans to allow for signal equilibration. Visual screening of the functional volumes revealed that none of the subjects showed indications of gross movement (> 1 voxel). The skull and other non-brain areas were extracted from the anatomical and functional scans using FSL's script Brain Extraction Tool (BET). Motion Correction using FMRIB's Linear Image Registration Tool (MCFLIRT) was performed on each functional scan. The volumes were spatially smoothed with a 5 mm full-width at half-maximum filter, and a 60s high-pass temporal filter was applied. These functional images were then co-registered with the anatomical images using FMRIB's Linear Image Registration Tool (FLIRT).First-level fMRI analysis of single subject data was performed using FMRI Expert Analysis Tool (FEAT) Version 5.98. The explanatory variables (EVs) for thermal stimuli were entered using the recorded temperature traces for each subject. Subjects were spatially normalized to the MNI152 brain for group analysis. Group activation maps were generated by fMRI expert analysis tool (FEAT) fMRIB's Local Analysis of Mixed Effects (FLAME). For all of the functional comparisons, the group statistical parametric maps were threshold using a Gaussian Mixture Model (GMM) technique, a multiple comparisons-based analysis generally used for unsupervised classification of data into multiple categories (Pendse et al., 2007; Moulton et al., 2007). Single trial averages (STAs) were calculated using in-house programs. [...] Subcortical volumetric segmentation was performed with the Freesurfer image analysis software ( The initial processing steps included (i) Motion correction and averaging of the two volumetric T1-weighted MPRAGE images, (ii) Removal of non-brain tissue using a hybrid watershed/surface deformation procedure [], (iii) Automated Talairach transformation, (iv) Segmentation of the subcortical white matter and deep gray matter volumetric structures (including hippocampus, amygdala, caudate, putamen, ventricles) [,], (v) Intensity normalization []. Subsequent to these processing steps, the volumes were labeled based on both subject-independent probabilistic atlas and subject-specific measured values [,]. These labels were then mapped into Talairach space to achieve point-to-point correspondence for all subjects. This method uses both intensity and continuity information from the entire 3-dimensional high resolution structural volume in segmentation. A univariate analysis of variance for each of the segmented volumes was performed separately using IBM SPSS 19.0 statistics package to assess the differences between the two groups of migraine patients while accounting for the differences in the cranium size [] and age as additional regressors. […]

Pipeline specifications

Software tools FreeSurfer, SPSS
Applications Miscellaneous, Connectivity analysis
Organisms Homo sapiens
Diseases Migraine Disorders, Embolism, Paradoxical