Computational protocol: A Longitudinal Study of Disability, Cognition and Gray Matter Atrophy in Early Multiple Sclerosis Patients According to Evidence of Disease Activity

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Protocol publication

[…] Information about radiological progression was extracted from the routinely reported evaluations of the cerebral MRI scans made by neuroradiologists at the hospital, and categorized as either radiological progression or no radiological progression by the first author (GON).The original scans from both time points were visually inspected to assure good quality before the segmentation. For volumetric analyses, the baseline images were reprocessed, so that both baseline and follow-up images of patients and controls were processed with the same software version, Freesurfer version 5.3 ( To extract reliable volume estimates, images were automatically processed with the longitudinal stream in Freesurfer []. The processing steps included registration of the scans to a common atlas, ensuring that minor differences in head positioning in the scanner would not affect the results. An unbiased within-subject template was created using robust, inverse consistent registration []. Several processing steps, such as skull stripping, Talairach transformations, atlas registration, spherical surface maps and segmentations were then initialized with common information from the within-subject template, in order to increase reliability and statistical power []. After segmentation, one scan was discarded because of obvious segmentation mistakes. Data from the further scans were transferred to SPSS for statistical analyses. […]

Pipeline specifications

Software tools FreeSurfer, SPSS
Applications Miscellaneous, Magnetic resonance imaging
Organisms Homo sapiens
Diseases Multiple Sclerosis, Multiple Sclerosis, Relapsing-Remitting