Work in progress…

Currently available pipelines for T1/T2 ratio:

QUNEX implementation of HCP pipeline

In Neurosmog:

  1. HCP uses FS 6 (nie uznają FS 7)
  2. Official HCP pipeline supports multiple T1ws
  3. HCP BIDS APP is availble from Neurodesk (ml bidsapphcppipelines)
    1. HCP BIDS APP uses HCP pipeline ver. 4.3.0 - https://github.com/bids-apps/HCPPipelines/blob/ae3ea7b799f3a5cd5dc077c46420557f5c476cd6/Dockerfile#L99
  4. HCP pipeline 5.0 now supports bias correction of T1/T2 ratio
  5. Seems reasonable to use qunex as a workbench - https://qunex.readthedocs.io/en/latest/wiki/UsageDocs-HCPPreprocessGeneral.html
  6. HCP does not include a pediatric atlas even in HCP-D 5-21 y/o implementation. Mathew Glasser not directly refuses to use them - https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/8NzmgTB8r9I/m/2BD1leclAgAJ
  7. Psuedo bias field correction (as implemented in ver. 5.0) would need fMRI (SbRef) and fieldmaps available and preprocessed from the beginning. Then it takes another scripts to be executed AFTER PostFS i.e. https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/2sXI05NnjaM/m/rAQoXikLDQAJ. As we have B1+ scans, we can use direct correction without other prerequisites (?)
  8. Original trransmit bias correction batch - https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/TransmitBiasBatch.sh
  9. Google groups feed - https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/2sXI05NnjaM/m/Cdslz0ajAAAJ
  10. TODO - add b1-map to dcm2bids config as described here https://bids-specification.readthedocs.io/en/v1.6.0/99-appendices/11-qmri.html#tb1tfl-and-tb1rfm-specific-notes
  11. QUNEX forum - https://forum.qunex.yale.edu/t/hcp-transmitbias-pipeline/1289?u=bkossows
  12. Group Mylein Map - required in the TransmitBias Pipeline

Partial.MyelinMap_GroupCorr_MSMAll.32k_fs_LR.dscalar.nii