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Repo that deals with datalad aspects for internal use
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`spine-generic-processed`: explain modalities in README #145

Open kousu opened 3 years ago

kousu commented 3 years ago

The current README says

This dataset is a processed version of spine-generic/data-multi-subject using preprocess_data.sh. This dataset follows the BIDS convention.

Processing steps inlcude:

For T1w and T2w :

  • Resampling to effective resolution

  • Reorient to RPI

  • Remove suffix _RPI_r

  • For T2star:

  • Compute root-mean square across 4th dimension (if it exists)

  • Remove suffix _rms

For DWI:

  • Generate mean image after motion correction: sub-XXX_rec-average_dwi.nii.gz
  • Remove intermidiate files

The dataset includes more than just T1w, T2w, T2* or dwi, it also includes files marked acq-{{T1w,MT{off,on}}_MTS. What are these?

Maybe it would help if these were explained briefly in the README, along with the other modalities too. Is modality the right word for all of these?

kousu commented 3 years ago

I found:

Linking to these pages would almost be enough, but they don't explain what MTon or MToff or _MTS mean. This mentions MTS in a list of file collection types but doesn't explain what it is.

jcohenadad commented 3 years ago

The dataset includes more than just T1w, T2w, T2* or dwi, it also includes files marked acq-{{T1w,MT{off,on}}_MTS. What are these?

these are magnetization transfer data-- indeed, the README should include these

joshuacwnewton commented 3 years ago

these are magnetization transfer data-- indeed, the README should include these

Further reading: https://radiopaedia.org/articles/magnetisation-transfer-1

SCT also has tutorials that use MT images, if you're curious about an example of what they can be used for in practice. (I believe MTon/MToff are equivalent to the MT1/MT0 convention SCT uses, if you've seen that before).

Linking to these pages would almost be enough, but they don't explain what MTon or MToff or _MTS mean. This mentions MTS in a list of file collection types but doesn't explain what it is.

I googled "_MTS" site:https://bids-specification.readthedocs.io and found this page. Specifically:

Suffix Linking entities Application Description
MTS flip, mt Magnetization transfer saturation This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle (Helms et al. 2008).
sandrinebedard commented 3 years ago

ok, I will modify the README!

kousu commented 3 years ago

Thanks Sandrine!

sandrinebedard commented 3 years ago

@kousu I've updated the README on the branch sb/update_readme

It is now:

This dataset is a processed version of spine-generic/data-multi-subject using preprocess_data.sh. This dataset follows the BIDS convention.

The dataset includes the following modalities (see the acquisition protocol):

  • T1w (3D, 1 mm)
  • T2w
  • T2star
  • Magnetisation Transfer data:
    • MTon_MTS:
    • MToff_MTS:
    • T1w_MTS:
  • DWI: Diffusion Weighted Imaging

Processing steps inlcude:

For T1w and T2w :

  • Resampling to effective resolution

  • Reorient to RPI

  • Remove suffix _RPI_r

  • For T2star:

  • Compute root-mean square across 4th dimension (if it exists)

  • Remove suffix _rms

For DWI:

  • Generate mean image after motion correction: sub-XXX_rec-average_dwi.nii.gz
  • Remove intermidiate files