Marieke van Rosmalen

Quantitative MRI characteristics of chronic inflammatory neuropathies 95 6 signal to noise ratios (SNR). Therefore, we performed DTI twice in all the following participants to improve data quality. These two acquisitions were combined in a later stage during data processing. We exclude scans with low quality, for example due to movement or the presence of artifacts, from further processing. Table 6.1 MRI parameters Parameter DTI T2 mapping T1 DIXON 3D TSE Acquisition 2D SE-EPI 2D TSE 3D FFE 3D TSE Field of view 240*180*150 mm 3 240*180*52.5 mm 3 288*288-200.25 mm 3 336*336*170 mm 3 Matrix size 96*71 96*96 192*192 224*223 Slice thickness 2.5 mm 2.5 mm - - Voxel size 2.5*2.5*2.5 mm 3 2.5*2.5*2.5 mm 3 0.75*0.75*0.75 mm 3 0.75*0.75*1 mm 3 Echo time 60 ms 7.6 ms 1.186 ms 206 ms Number of echoes - 17 3 - Repetition time 8595 ms 3242 ms 5615 ms 2200 ms Flip angle - - 16 o - Turbo spin echo factor - - - 76 Sensitivity encoding factor 2.5 2.3 2 (AP); 1 (FH) 3 (RL); 1.5 (AP) Fat suppression SPAIR - - SPIR Gradient directions 37 - - - b values (s/mm 3 ) 0, 50, 100, 150, 300, 400, 600 - - - Acquisition time 05:43 minutes 04:45 minutes 01:56 minutes 03:59 minutes Abbreviations: DTI = diffusion tensor imaging; TSE = turbo spin echo; SPAIR = spectral attenuated inversion recovery; SPIR = spectral presaturation with inversion recovery; SE EPI = spin echo-echo planar imaging; FFE = fast field echo; mm = millimeter; ms = milliseconds; AP = anterior/posterior; FH = foot/head; RL = right/left. Data processing DTI We processed all DTI data semi-automatically, using a two-step custom-build processing pipeline based on the diffusion toolbox ExploreDTI which allows visualization of the spinal nerve roots, segmented tract analysis and extraction of diffusion parameters. 27 An overview of the pipeline is shown in Figure 6.1 . Before processing, we resampled the 3DTSE SPIR to a 2x2x2 mm 3 isotropic resolution. Subsequently, we manually drew a rough mask of the brachial plexus area using ITK SNAP (10 minutes per data set). 28 These masks were drawn in the resampled 3D TSE SPIR and in the diffusion-weighted image to guide the registration and fiber tract selection ( Figure 6.1B ). The first automated part of the