Beginner: Connectome pipeline (Updated)

Antonin_Skoch · January 4, 2017, 10:32pm

I have very good experience on skull-stripping in structural data with PreFreeSurfer HCP pipeline:

Washington-University/HCPpipelines/blob/master/Examples/Scripts/PreFreeSurferPipelineBatch.sh

#!/bin/bash

#~ND~FORMAT~MARKDOWN~
#~ND~START~
#
# # PreFreeSurferPipelineBatch.sh
#
# ## Copyright Notice
#
# Copyright (C) 2013-2018 The Human Connectome Project
#
# * Washington University in St. Louis
# * University of Minnesota
# * Oxford University
#
# ## Author(s)
#
# * Matthew F. Glasser, Department of Anatomy and Neurobiology,
#   Washington University in St. Louis
# * Timothy B. Brown, Neuroinformatics Research Group,

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You can switch off gradient nonlinearity correction or readout distortion correction of structural images if you do not want to (or do not have required additional data for that).

AmirHussein · September 11, 2017, 1:36pm

Hi Elijah,

Thanks for the pipeline you’ve presented here. It’s actually a nice and well-described pipeline. I have a question. Is there something that you didn’t use the SIFT output as the tck2connectome input here?

tck2connectome i.tck i_nodes.mif i_connectome.csv -zero_diagonal

i.tck is the tckgen output, i_sift.tck is the SIFT’s.

Bests,
Amir