Dear all,
Do you know the SUMMARY FG parameters in IQM of functional images in MRIQC are related to what?
Thanks,
Soroor
Hi @soroor. Good question. FG usually stands for “foreground” (e.g., anatomical.snr mentions foreground: IQMs for structural images — mriqc 0.1 documentation). As to where “foreground” is defined, I’m not sure that a definition is in the docs. Based on looking through the source, I think it refers to everything inside a brain mask (i.e., the foreground is all voxels containing either white matter, gray matter, or cerebrospinal fluid edit: foreground mask does not include CSF).
Does that help?
Hi
thank you for your useful reply, I need more information about the parameters of IQMs, on this page( IQMs for structural images — mriqc 0.1 documentation) some parameters don’t explain very much or at all, for example, spacing_tr or size_x. do you know any site or any document for getting more information about these parameters?
thanks,
Soroor
Hi @soroor. Unfortunately, I’m not aware of any detailed explanation on each of these parameters. This is a case where it may be necessary to read the source code to know exactly what’s going on (https://github.com/poldracklab/mriqc). I know that’s not super helpful, but do feel free to keep asking about specific metrics that the docs and references don’t give information on.
The cases of spacing_tr and size_x happen to be straightforward; spacing_tr is the TR of the scan (the amount of time that passed between repeated collections of a slice), and size_x is the dimension of the data along the first axis. If you have fsl installed, these are the same values that you’d see when running fslhd
One more note, while searching for something else on the github repo, I came across this issue, which points to an NDA data dictionary that appears to at least have a note on each metric. Though, that issue is a few years old, which means mriqc may have been updated since it the dictionary was created.