Name: minc-bpipe-library
Owner: Kimel Family Translational Imaging-Genetics Research Lab
Description: Library of bpipe implemented commands commonly applied to minc datafiles, suitable for importing into other pipelines
Created: 2015-01-26 19:04:47.0
Updated: 2014-11-19 22:32:04.0
Pushed: 2015-03-20 23:33:31.0
Homepage: null
Size: 123
Language: null
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minc-bpipe-library provides a set of chainable minc file processing functions to (pre)process data.
It requires http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit, https://stnava.github.io/ANTs/, and https://github.com/ssadedin/bpipe/
To control which stages are run, edit pipeline.bpipe and add stage names using “+” to the “run” stage.
Stages are listed in the minc-library.bpipe, correction stages such as denoising, n3 and n4, and normalize
should be run before any other stages. Typically after this linear_register would be run, which will
allow other processing such as VBM, cutneck, deface and beast.
For convenience, “segments” have been defined for some processing jobs (beast, cutneck, VBM) which are multi-step. These will conflict with each other if you try to combine them, so instead you must specifiy their individual stages.
Stage options have been chosen based on best pratices from publications where applicable but can be changed.
Once you have defined your stages, you can run your pipeline on the SGE cluster with:
dule load bpipe #needed to run bpipe
dule load minc-toolkit/1.0.04 #needed for most stages
dule load ANTs/2.1.0 #Needed for n4correct
ose n to be the smaller of (number of input files, 240)
ipe run -n<number> -d /path/to/store/outputs /path/to/pipeline.bpipe /path/to/inputs/*mnc
Output filenames from bpipe will be of the form <inputname>.stage1.stage2.stage3.ext where the last stage
name will be the last run. commandlog.txt will be generated by bpipe describing all the commands run for
the pipeline. This is a very good file to keep around as as a note of what happened to your data.
Some stages produce both mnc files and xfm files, see the $output variables for what is generated.