Computational protocol: Transient effects of tumor location on the functional architecture at rest in glioblastoma patients: three longitudinal case studies

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Protocol publication

[…] The data preprocessing pipeline consists of several steps performed using a combination of tools including dcm2nii [], ITK-SNAP [], the FMRIB’s Software Library (FSL) [] and custom homemade MATLAB scripts []. Semiautomatic tumor segmentations were done with ITK-SNAP based on anatomical images and reviewed by an expert radiologist. Preprocessing of the functional data consisted of excluding the first two volumes of each experimental run to allow the fMRI signal to reach steady state and scrubbing of the volumes with motion related artifacts. FEAT tool was used for preprocessing (motion and slice time correction, brain extraction, 5 mm smoothing, intensity normalization) and registration to T1-weighted image (6° of freedom) and 2 mm MNI152-template (12° of freedom) were based on FSL’s FLIRT and FNIRT. […]

Pipeline specifications

Software tools MRIcron, ITK-SNAP
Applications Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Neoplasms, Glioblastoma, Glioma, Neoplasms