Calculating theoretical T1-weighted MRI images with arbitrary value of inversion time (TI) based on previously acquired spin echo multi-slice experiment with inversion recovery (SEMS-IR) .fid (Agilent) data. This functionality can be used to calculate many T1-weighted images, with small TI step, to find the TI value for the optimal image contrast after performing MRI imaging for just few TI values to save time.
Calculating theoretical T2-weighted MRI images with arbitrary value of echo time (TE) based on previously acquired multi-echo multi-slice (MEMS) .fid (Agilent) data. This functionality can be useful when TE needed to obtain optimal image contrast is outside the hardware limits. This can happen when using large image matrix while imaging structures with short T2.
The script can also be used for calculating T1, T2 and M0 maps without calculating theoretical images.
The user provides the data folder location and a list of desired TE or TI values. If the list is empty, only the parametric maps are calculated. The script automatically imports the data with all the parameters needed and performs computations. The user can change the value of glob_var parameter to save the maps and/or the images in global Python variable for further use (instead of just saving the image files).
- Python script TI_TE_wish.py.
- Sample FID data in sems_20190407_07.fid and mems_20190519_01.fid folders.
- Sample results in Theoretical_MRI_T1w and Theoretical_MRI_T2w folders.
- Graphical abstract graph_abst.png.
Beata Wereszczyńska, Alcohol-fixed specimens for high-contrast post-mortem MRI, Forensic Imaging, Volume 25, 2021, 200449, ISSN 2666-2256, https://doi.org/10.1016/j.fri.2021.200449. (https://www.sciencedirect.com/science/article/pii/S2666225621000208)
The software is licensed under the MIT license. The non-software content of this project is licensed under the Creative Commons Attribution 4.0 International license. See the LICENSE file for license rights and limitations.
TIandTE_wish - Calculating theoretical MRI images with both inversion time (TI; T1-weighting) and echo time (TE; T2-weighting) of choice, from separate T1-weighted and T2-weighted sets of images. This functionality can be used to visualise how inversion recovery images would look like if TEmin could be shorter or how the images' contrast will change after TE increase (e.g. due to larger image matrix). Works with Agilent SEMS (with IR) and MEMS .fid data acquired for the same slices and matrice size, (https://github.com/BeataWereszczynska/TIandTE_wish).
T1wIR_to_T1wSR - Calculating T1-weighted saturation recovery (SR) MRI images for arbitrary values of repetition time (TR) from a set of T1-weighted inversion recovery (IR) experimental MRI images. The script can also be used for calculating T1 and M0 maps without calculating theoretical images. Works with Agilent .fid data (https://github.com/BeataWereszczynska/T1wIR_to_T1wSR).
MRI_k-space-derived_details_edges - k-space based details/edges detection in MRI images with optional k-space based denoising and detail control (data import suitable for Agilent FID files, three binarization methods to choose from), https://doi.org/10.5281/zenodo.7388435 (https://github.com/BeataWereszczynska/MRI_k-space-derived_details_edges).
Swelling_tablet_fronts_D_k_from_MRI_T2_or_img - Tool for characterizing the swelling of tablets immersed in a solution. Creates time plots and calculates eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or (properly contrasted, e.g. T2-weighted) MRI images in FDF (file format native for Agilent MRI scanners) or Text Image format. This software is suitable for swelling matrix tablets forming a membrane-like structure in contact with the solution in which they are immersed, https://doi.org/10.5281/zenodo.7262466 (https://github.com/BeataWereszczynska/Swelling_tablet_fronts_D_k_from_MRI_T2_or_img).