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Pipeline publication

[…] dwidth = 1116 Hz/Px, partial Fourier 6/8, GRAPPA acceleration with iPAT factor of 3, 300 volumes per scan). In the first of these 2 sessions, an additional short structural scan (11 min) was acquired using the MP2RAGE sequence with similar parameters as above but an isotropic resolution of 0.7 mm. The uniform T1-weighted (T1w) image generated from this scan was used as an intermediate registration target to project the resting-state data into the space of the high-resolution T1 map and will be referred to as the “low-resolution T1w image.”, All data processing and analyses were performed on Linux servers running Ubuntu 12.04.5 LTS. The following software tools were used for data processing: CBS Tools (v3.0, ) as a plugin for MIPAV (v7.0.1, ) and JIST (v2.0, ), ANTs (v2.1.0, ), Nipype (v0.11.0, ), Nilearn (v0.2.3, ), Meshlab (v1.3.0, meshlab.sourceforge.net), Freesurfer (v5.3.0, ; ), and AFNI (v16.1.28, ). Custom scripts were written in Python 2.7 using numerous libraries (; ; ; ; ; ; ). More details and all code can be found at https://github.com/juhuntenburg/myelinconnect., Preprocessing of the high-resolution T1 maps was carried out using CBS Tools (Fig. ). Tissue segmentation and reconstruction of white matter (WM), midcortical, and pial surfaces was performed as described previously (). Cortical thickness between the WM and pial surface was calculated. For each subject, 9 intracortical surfaces were generated between the WM and […]

Pipeline specifications

Software tools CBS Tools, MIPAV, JIST