[ENH] Various proposed changes to diffusion derivatives #205
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Following on from ea2bc96. - Fix grammattical error in description of DWI JSON. - Modify description of recommended NODDI model output. - For "fwDTI" model, separate tensor coefficients and free water fraction data into two separate NIfTI images. - For DTI model, include iterative weighted least squares as an option, and separate RESTORE (outlier rejection) as being a separate parameter rather than a method of fitting. - For CSD model, offer two mechanisms for specifying the response function; also remove MRtrix 0.2 SH basis, and remove "none" from NonNegativityConstraint (as without a non-negativity constraint, it would not be CSD). - Provide additional examples for DWI model outputs. - Remove NODDI parameters from "model-derived maps", as these are re-classified as fundamental model output parameters. - Remove DECFA from "model-derived maps", and instead define "directionally-encoded colour maps" as a different form of model-derived map, since any scalar map can be augmented with DEC. - Add "Count" as a compulsory parameter for tractography output. - For tractography output, provide three distinct dictionaries within the JSON: "Constraints" (ROIs and anatomical tissue constraints), "Parameters" (for parameters specific to the streamlines tractography algorithm), and "Seeding" (since determining streamline seeds is in fact independent of the particular tractography algorithm and parameters). Field "TerminationCriterion" was removed in this process as it is common for there to be more than one mechanism by which streamlines are terminated. Possibilities for streamline seeding have been more broadly generalised as part of this process.
Follows from �18dc84fc.
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Just want to call the attention of: @oesteban, @francopestilli, @jchoude, @arokem. I believe this is one of two outstanding issues on the derivatives BEP. |
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For myself, I'll get on this on Friday night. Sorry for the lag. |
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Hi @Lestropie and @effigies thanks for your patience. I went through this and have only small comments (mainly typos).
Thanks for all this work @Lestropie I think this version would be good to merge in the spec. I quickly went back through the old discussions on the previous PR, and everything seems in line with the overall discussions. I don't see anything here that isn't in line with the spirit of the Diffusion derivatives.
Thanks again!
| | `DKI` | Diffusion kurtosis imaging (Jensen et al., 2005) | 4D image with Dxx, Dxy, Dxz, Dyy, Dyz, Dzz, Wxxxx, Wyyy, Wzzzz, Wxxxy, Wxxxz, Wxyyy, Wyyyz, Wxzzz, Wyzzz, Wxxyy, Wxxzz, Wyyzz, Wxxyz, Wxyyz, Wxyzz; Where D is the diffusion tensor and W is the kurtosis tensor. | | ||
| | `WMTI` | White matter tract integrity (Fieremans et al., 2011) | 4D image with Dxx, Dxy, Dxz, Dyy, Dyz, Dzz, Wxxxx, Wyyy, Wzzzz, Wxxxy, Wxxxz, Wxyyy, Wyyyz, Wxzzz, Wyzzz, Wxxyy, Wxxzz, Wyyzz, Wxxyz, Wxyyz, Wxyzz, Dhxx, Dhxy, Dhxz, Dhyy, Dhyz, Dhzz, Drxx, Drxy, Drxz, Dryy, Dryz, Drzz, AWF; where D is the diffusion tensor, W is the kurtosis tensor, AWF is the additional axonal water fraction parameter | | ||
| | `CSD` | Constrained Spherical Deconvolution (Tournier et al. 2007; Descoteaux et al. 2009) | 4D image with spherical harmonic (SH) coefficients (number of volumes and their ordering depends on the model maximal degree and basis set, specified in the sidecar) | | ||
| | `NODDI` | Neurite Orientation Dispersion and Density Imaging (Zhang et al. 2012, Daducci et al., 2015) | Three 3D images, with <parameter> equal to {`ICVF`,`OD`,`ISOVF`}: ICVF is the “intracellular volume fraction” (also known as NDI); OD is the “orientation dispersion” (the variance of the Bingham; also known as ODI); ISOVF is the isotropic component volume fraction (also known as IVF). Additionally a vector-valued map with the parameter name "`direction`" may provide the XYZ direction of the estimated fibre orientation. | |
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It seems like the <parameter> tag does not render correctly, at least when using the View file rendering option directly in Github.
| - `Basis` : {`MRtrix 0.2`,`MRtrix3`,`DESCOTEAUX`} | ||
| - `Tissue` : string | ||
| - `SphericalHarmonicDegree` : value | ||
| - `ResponseFunctionZSH` : values (1 row per unique *b*-value as listed in "`Shells`"; 1 column per even harmonic degree starting from zero) |
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I know this is from the comments on the previous review (the one targeting Chris's branch), but I agree with the options as defined now.
| - `ResponseFunctionOrder` : value | ||
| - `ResponseFunction` : \[1:response_function_order_value,b0mean\] | ||
| - `Basis` : {`MRtrix 0.2`,`MRtrix3`,`DESCOTEAUX`} | ||
| - `Tissue` : string |
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Should this be a controlled vocabulary, listing the possible tissue types?
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hi @jchoude thanks, how would you change this specifically?
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Just wondering if we should have a list of possible tissues and the spelling, like [white|gray|csf], to avoid people writing the same tissue type in various ways , eg: 'white matter', 'WM', 'white', etc.
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I'd be open to a limited controlled vocabulary; i.e. have pre-defined strings recommended for use, but still permit use of items not in the vocabulary. While MSMT is most commonly done with WM / GM / CSF tissues, it's in no way obliged to use such, and in time there will be an increasing number of use cases that don't conform to such. Is there an appropriate syntax for such in the spec?
Also note that I would generally expect an abbreviated name of the tissue to appear in the file name, probably under the "desc-" tag. So the "Tissue" string in the JSON is in one way redundant; but conversely it does give the opportunity for a more verbose name than what would be crammed into the filename.
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Yes, rethinking about it we might not want to add another vocabulary at this point. Let's leave it like that.
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Ideally this should be consistent with ROI names for time series in
functional derivatives.
…On Tue, Apr 23, 2019, 09:03 Jean-Christophe Houde ***@***.***> wrote:
***@***.**** commented on this pull request.
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In src/05-derivatives/05-diffusion-derivatives.md
<#205 (comment)>
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- - `SphericalHarmonicOrder` : value
- - `ResponseFunctionOrder` : value
- - `ResponseFunction` : \[1:response_function_order_value,b0mean\]
- - `Basis` : {`MRtrix 0.2`,`MRtrix3`,`DESCOTEAUX`}
+ - `Tissue` : string
Just wondering if we should have a list of possible tissues and the
spelling, like [white|gray|csf], to avoid people writing the same tissue
type in various ways , eg: 'white matter', 'WM', 'white', etc.
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- Minor spelling & grammar fixes. - In "scalar maps" section, expand out the different parameters to be derived from the ball-and-stick(s) model. - Provide more accurate link to MRtrix3 tracks file format.
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Some more updates in 74ff6d0. One other thing that caught my eye was the labelling of "BedpostX" as a model. Personally I see this as a software command that fits a particular model, with that model being "Ball-and-sticks", with the command then applying bootstrapping over the top of that. It might however be worth getting this PR over and done with and then proposing this change separately. |
- Fix use of superscripts in "Scalar maps" table. - For "Units" field in tractography JSON file, list possible values in the same format as that used elsewhere in the document.
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I reviewed your new changes and they all address the few last comments. I agree with you about To me, this looks good to go. I currently cannot merge, since I am not a BEP leader, but I would happily do so if that was the case. Thanks Robert (@Lestropie ) for all this work! |
A duplicate of chrisgorgo#6 as requested by @chrisgorgo. A large volume of relevant discussion can be found in the original PR; discussion related to finalisation of the proposed changes can be made here.