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NIST MNI minipipeline

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Xuan Mai PHAM edited this page Feb 12, 2024 · 7 revisions

T1w and FLAIR scans processed by NIST (Neuro Imaging and Surgical Technologies) -MNI mini pipeline

Contents of this directory

The documentation was provided by Vladimir S. FONOV, research associate at NIST.

The modalities of out/sub-<id>/ses-2/tal/tal_sub-<id>_ses-2_<modality>.mnc are:

  • T1w
  • flair
  • brain

These files contain anatomical MRI scans of UK Biobank after processing with in-house tools, based onminc-toolkit-v2version 1.9.17

Processing steps for the T1w scan include:

  1. nonuniformity correction using N4

  2. linear intensity normalization using histogram to match MNI-ICBM152 2009c intensity ranges

  3. linear stereotaxic registration to MNI-ICBM152 2009c space using bestlinreg tool version from 20180117

  4. linear warping into MNI-ICBM152 2009c space

  5. brain-masking using BEaST

  6. second nonuniformity correction usingN4with BEaST brain mask

  7. second linear intensity normalization

FLAIR scans

They were linearly (rigid body) co-registered with T1w scans and warped using the concatenated transform of FLAIR and T1w

There are also .xfm files: out/sub-<id>/ses-2/tal/tal_xfm_sub-<id>_ses-2.xfm - describes linear (9 parameter) transformation from native to MNI-ICBM152 2009c space for T1w scans

out/sub-<id>/ses-2/tal/tal_sub-<id>_ses-2_brain.mnc - was produced using an in-house brain segmentation tool (deep learning based) from out/sub-<id>/ses-2/tal/tal_sub-<id>_ses-2_t1w.mnc

Questions or Issues?

For any questions or issues related to the registration process for accessing the UK Biobank data through the McGill agreement, please contact the NeuroHub team by email at support@neurohub.ca.

For any questions or issues specifically related to accessing the NeuroHub portal or using any of the NeuroHub features and functionalities, please contact the NeuroHub team by email at support@neurohub.ca.

Table of Contents

1. Getting started

  1. Get a NeuroHub account
  2. Obtain UKBiobank access

2. Using NeuroHub

  1. Available Tools and Datasets
  2. Access NeuroHub
  3. Creating a project
  4. LORIS Data Query TooL(DQT)
  5. Jupyter Notebooks in NeuroHub
  6. Messaging in NeuroHub
  7. Accessing the Canadian Open Neuroscience Platform(CONP) datasets
  8. Accessing the HCP(Human Connectome Project) datasets
  9. Accessing the UK Biobank dataset
  10. Accessing the ABCD dataset
  11. Accessing the OpenNeuro dataset

3. Examples

  1. Analyses of structural data
  2. Cellranger Count
  3. scrNAbox
  4. BraTSPipeline

4. Supplementary Information

5. Direct access to the UK Biobank data

  1. Available Data
  2. An example of extracting ICD codes from UK Biobank tabular data
  3. Accessing Imaging Data

6. NeuroHub and Machine Learning

7. Acknowledging NeuroHub

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