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Ex Vivo MRI in Frontotemporal Lobar Degeneration

Cite this dataset

Tisdall, Dylan (2021). Ex Vivo MRI in Frontotemporal Lobar Degeneration [Dataset]. Dryad.


Ex vivo MRI of 7 human hemispheres, acquired at 7 T using multi-echo gradient recalled echo imaging. Details of these samples are presented in the associated manuscript.


Samples were placed in Fomblin (California Vacuum Technology; Freemont, CA), a proton-free fluid with volume magnetic susceptibility close to that of tissue. Samples were enclosed in either custom-build cylindrical holders or plastic bags, and then left to rest for at least two days to allow air bubbles to escape from the tissue. Depending on their size, samples were scanned using either a custom-built small solenoid coil or a custom-modified quadrature birdcage (Varian, Palo Alto, CA, USA) coil. These transmit/receive coils were attached to a two-channel transmit-receive adapter (Stark Contrast, Erlangen, Germany). The smallest coil was chosen that could hold each sample, tuned/matched by hand, and then placed into our whole-body 7 T scanner (MAGNETOM Terra, Siemens Healthineers, Erlangen, Germany) using plastic shims under the coils to position the sample near isocenter.

MRI data were acquired with a 3D-encoded, 8-echo gradient-recalled echo (GRE) sequence with non-selective RF pulses. To maintain readout polarity and minimize distortions due to field inhomogeneity, each readout was followed by a flyback rephrasing gradient. The final echo was followed by an additional completely rephrased readout to measure frequency drifts. Each line of k-space was acquired with multiple averages sequentially before advancing to the next phase-encode step. Common parameters for the sequence were: 280 µm isotropic resolution, 25° flip angle, 60 ms repetition time (TR), minimum echo time (TE) 3.48 ms, echo spacing 6.62 ms, bandwidth 400 Hz/px. The field of view was adapted to each sample, and subsequently TRs and TEs were slightly modified based on the necessary readout duration. Total scan times were 8-10 hours for each sample.

Images were reconstructed using the vendor’s on-scanner reconstruction software which automatically corrected the global frequency drift, combined the signal averages in k-space, and produced magnitude images for each echo.

Usage notes

Image data is in DICOM format, organized with per-patient directories. Imaging data dimensions are described in the DICOM data headers. Details of the patients' clinical and demographic information is included in the associated manuscript.


National Institute of Neurological Disorders and Stroke, Award: R01NS109260

National Institute on Aging, Award: P01AG017586 P01AG066597 P30AG10124 R01AG054519

Penn Institute on Aging

Robinson Family Foundation

Wyncote Foundation

Penn Institute on Aging

Robinson Family Foundation