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Pipeline publication

[…] tatistical analysis. Lilliefors goodness-of-fit test of all subjects was employed to assess whether all subjects were from a normal distribution. Then we also compared the ReHo results between t1 and t2 by performing voxel-based paired t tests in both groups separately. The P < 0.05 was deemed significant for the AlphaSim correction (the parameters used in the AlphaSim program: cluster size >1458mm3, spatial smoothness = 4, rmm = 4, a whole-brain mask provided by DPARSF). Based on the paired t test findings, the abnormal ReHo brain regions were identified as regions of interest (ROIs), the mean zReHo value of each ROI for all the subjects was extracted., We used a pipeline tool called PANDA (http://www.nitrc.org/projects/panda/) [] to process data by the following steps:, 1) Converting format: Dicom files of DTI raw data were converted into Nifti format during this step. The dcm2nii tool embedded in MRIcron accomplished this task., 2) Estimating the brain mask: This step yielded the brain mask by using the bet command of FSL (FMRIB Software Library v5.0) []. The brain mask was required for the subsequent processing steps. Here, the b0 image without diffusion weighting was used for the estimation., 3) Cropping the raw images: To reduce the memory cost and speed up the processing in subsequent steps, we cut off the non-brain space in the raw images to reduce the image size. The acquired brain mask was used to determine the borders of the brain along the three dimensions. The fslroi command of FSL was then applied to remove the non-brain spaces., 4) Correcting for the eddy-current effect: Eddy-current induced distortion of diffusion weighted images (DWI), as well as the simple head-motion during scanning, can be cor […]

Pipeline specifications

Software tools PANDA, MRIcron, FSL