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  1. MBM.py cookbook

    This page provides examples of MBM.py runs on different kinds of data. Why is the --pipeline-name argument is so important... The names of files … ) and when you rerun it, supply it as follows: MBM.py --pipeline-name=pipeline-21-11-2016-at-16-11-33 [rest of your command] What does --maget-no-mask really mean
    MICe PublicJul 06, 2017
  2. File equivalents between MICe-build-model.pl and MBM.py

    Equivalents for MBM.py version 1.10 (and older) MBM.py is still under development. We are working on making sure that the filenames produced by MBM.py are intuitive (that's currently not yet the case). Here are the equivalents for any MBM.py version 1.10 or older (prior to October 31, 2014). Currently when you run
    MICe PublicOct 31, 2014
  3. Iterative Model Building (MBM 2.0)(MBM.py)

    design and documentation for MBM 2.0 can be found here. How to Use MBM 2.0 Using an Initial Model recipes on how to use MBM.py Quality Control on your pipeline
    MICe PublicJan 04, 2016
  4. Pydpiper on the SickKids HPF

    a pipeline See here for some detailed information on how to troubleshoot a pipeline: Troubleshooting pydpiper pipelines Example calls for MBM.py MBM.py cookbook … as follows: [bdarwin@hpclogin3 ~]$ screen [bdarwin@hpclogin3 ~]$ qlogin ... [bdarwin@qlogin1 ~]$ MBM.py ... # now press Control-"a" (to send a command to screen
    MICe PublicJun 30, 2021
  5. pydpiper_tutorial_I.pdf

    of brains in registration (subj.mnc/subj_mask.mnc) • No masks specified [Default] —> No masks used in registration but if running standard MBM.py, program grabs … Average MBM.py Example command - 224microns Default command - 56microns Directories and restart NOTE: Easiest to run the —restart command when in the same
    MICe Public / … / Using Pydpiper ApplicationsJul 03, 2014
  6. Pydpiper development - checklist

    Things to check when working on a new pydpiper release. Does this work? 63 incomplete MBM.py --help 64 incomplete asymmetry.py --help 65 incomplete … incomplete MBM.py cookbook Can we run the testbed? 69 incomplete Pydpiper Did we install on all systems? 70 incomplete HPF 71 incomplete MICe 72
    MICe PublicMar 17, 2017
  7. Pydpiper

    templates. MBM 2.0 Iterative Model Building (MBM 2.0)(MBM.py) MBM.py Newer, more flexible version of MICe-build-model. Registration chain Longitudinal … be tested by a combination of a MBM.py and a MAGeT.py pipeline. We have a set of test data containing two groups of brains (10 samples per group). The test bed
    MICe PublicApr 17, 2017
  8. Creating an Initial Model

    together using MBM.py and the bootstrap flag MBM.py \ --bootstrap \ --pipeline-name=bootstrap_b0 \ --subject-matter mousebrain \ --num-executors 30 … - this is the initial model's mask in native space You can now use this initial model in your registration. MBM.py \ --init-model=../spring-b0-DTI-80-micron-basket
    MICe PublicJun 29, 2021
  9. Pydpiper Virtual Machine

    , MBM.py, registration_chain.py and twolevel_model_building.py. The following sections describe how to run each of these and provides information to verify that the tests ran successfully. Testing the MBM.py application Open a shell, and run the following: cd /home/mice-pydpiper/Desktop/Pydpiper_test_data/ mkdir test_MBM
    MICe PublicJun 24, 2015
  10. Preferential Spatial Gene Expression in Neuroanatomy

    https://bic-mni.github.io/) and the RMINC package. Usage Neuroanatomy statistics can be performed usual way: MRI to obtain images, MBM.py to register to consensus (Iterative Model Building (MBM 2.0)(MBM.py)), RMINC to compute statistics on the log determinants at every voxel (RMINC). We can also load some useful libraries. library
    MICe PublicJul 14, 2021