[FIX] Split out tractography #9
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This PR splits the tractography section from the diffusion derivatives document, so that #5 is easier to merge. The new ``05-diffusion-derivatives-tractography.md`` file will remain orphaned, but kept there as a base for the time we tackle tractography. It shouldn't be merged into the derivatives branch until it is ready.
| ## Describing tractography | ||
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| Tractography normally generates one of two primary file types: tractograms or | ||
| NIfTi files containing maps. Tractograms are files containing a collection of |
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Is that really how nifti is capitalized?
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Should we say more about the file formats used to store tractograms?
| <pipeline_name>/ | ||
| sub-<participant_label>/ | ||
| dwi/ | ||
| <source_keywords>[_space-<space>][_desc-<label>][_subset-<label>]_tractography.[trk|tck|nii[.gz]] |
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| `subset` (optional) – A label descriptor for the the subset of streamlines | ||
| included in this file; if not specified, a whole brain tractography is assumed | ||
| (a tractogram). Example of subsets can be `short` if only short streamlines were |
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| (a tractogram). Example of subsets can be `short` if only short streamlines were | |
| (a full connectome). Example of subsets can be `short` if only short streamlines were |
Hey @francopestilli - is that the right terminology? "Tracogtram" refers to any subset, and "whole brain" is called "connectme" ?
| | LOCAL | NULL | Morris et al. (2008) | | ||
| | GLOBAL | UKF | Malcolm J-G. et al. (2009) | | ||
| | GLOBAL | SpinGlass | Fillard P. et al. (2009) | | ||
| | GLOBAL | ENS | Takemura et al. (2016) | |
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Does ENS really belong under the "global" category? Arguably, it can't generate anything that's not in one of the local tractograms in the ensemble?
| | **Key name** | **Description** | | ||
| | ------------------ | -------------------------------------------------------------------------------------------------------------------- | | ||
| | TractographyClass | REQUIRED. Allowed values: `local`, `global` | | ||
| | TractographyMethod | REQUIRED. Allowed values: `probabilistic`,`deterministic`,`eudx`,`fact`,`stt`,`null`,`ukf`,`spinglass`,`ens`,`other` | |
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We need to add "pft" (particle filtering tractography, see Girard et al., 2014)
| | ------------------ | -------------------------------------------------------------------------------------------------------------------- | | ||
| | TractographyClass | REQUIRED. Allowed values: `local`, `global` | | ||
| | TractographyMethod | REQUIRED. Allowed values: `probabilistic`,`deterministic`,`eudx`,`fact`,`stt`,`null`,`ukf`,`spinglass`,`ens`,`other` | | ||
| | Count | REQUIRED. integer | |
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Is this the number of streamlines stored in the file?
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Do you want this merged ASAP, and come back to these comments later? |
Yup, could you open a PR with your comments after this is merged? |
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Oh - no big green button! Looks like I don't have the permissions to merge this. :trombone: |
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Fixed that! |
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This PR splits the tractography section from the diffusion derivatives
document, so that #5 is easier to merge.
The new
05-diffusion-derivatives-tractography.mdfile will remainorphaned, but kept there as a base for the time we tackle tractography.
It shouldn't be merged into the derivatives branch until it is ready.