Structural MRI Acquisition and Preprocessing

Structural MRI acquisition and preprocessing has been previously described in detail (35 (link)). Briefly, T1-weighted (T1w) brain images were obtained with a 3.0T Philips Ingenia MRI system (1 mm isotropic resolution; TR, 8.1 ms; TE, 3.7 ms; flip angle, 8°; SENSE factor 2). FSL software (64 (link)) was used for bias field correction, tissue type segmentation and non-linear registration to the MNI152 template, using a lesion mask to improve registration for participants with stroke. Lesioned voxels in the native-space T1w image were temporarily filled with MNI template voxels (65 (link)) to enable automated structure labeling with FreeSurfer software (66 (link)). Lesioned voxels were then masked out of any structure labels.

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Boyne P., Doren S., Scholl V., Staggs E., Whitesel D., Carl D., Shatz R., Sawyer R., Awosika O.O., Reisman D.S., Billinger S.A., Kissela B., Vannest J, & Dunning K. (2022). Preliminary Outcomes of Combined Treadmill and Overground High-Intensity Interval Training in Ambulatory Chronic Stroke. Frontiers in Neurology, 13, 812875.

Publication 2022

Ingenia MRI system

Brain Stroke Tissue type

Corresponding Organization : University of Cincinnati Medical Center

Other organizations : University of Delaware, University of Kansas Medical Center

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Variable analysis

independent variables

MRI acquisition parameters (magnetic field strength, TR, TE, flip angle, SENSE factor)

dependent variables

Brain structure labels from FreeSurfer

control variables

MRI scanner (3.0T Philips Ingenia)
Image preprocessing steps (bias field correction, tissue type segmentation, non-linear registration to MNI152 template, lesion masking)

controls

Positive control: Lesioned voxels were temporarily filled with MNI template voxels to enable automated structure labeling with FreeSurfer software.
Negative control: Not explicitly mentioned.

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