Tissue fraction modulated ICVF and OD maps #218
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- AMICO produces ICVF and OD maps modulated by the non isotropic tissue fraction. This makes these available. - AMICO also produces (N)RMSE maps of the observed vs predicted signal. Saving these enables QC and other assessments of parameter selection.
Change naming structure so that "desc" isn't used.
|
It would probably be helpful to also have an output for the tissue fraction, but AMICO doesn't save that and I wasn't sure how to accomplish. Internally for AMICO, Left: ISOVF; Right: TF
|
|
It looks like the only remaining change is to the list of output files that is checked agaisnt in the Recon_AMICO test. I also noticed that you capitalized some of the parameters in the filenames, which is a breaking change. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes proposed in this pull request
Parker et al (https://doi.org/10.1016/j.neuroimage.2021.118749) proposed a tissue fraction modulation approach for NODDI metrics to reduce bias in ROI-associated mean computations. Modulation is just
{NDI,OD} * (1 - ISOVF). AMICO has these as output options through a global flag, along with the (N)RMSE maps from the fitting. This PR enables outputting of these 4 maps when running NODDI. Addresses #217.Includes citations for Parker et al and fixes some typos in the reports (generally) and in the AMICO specific reports as well.
Outputs from a test run:
Top row: Unmodulated ICVF (left) and OD (right)
Bottom row: Modulated ICVF (left) and OD (right)
Documentation that should be reviewed
Need to check docs. I tried to edit them but I'm not sure if I was successful. Probably also needs to be an explanation somewhere that the modulated maps should not, themselves be directly analyzed (per Parker et al) but rather the mean computed per region on them and then re-divided by the mean tissue fraction to get back to the original scale. Can do this when I know whether any of the documentation editing was successful.