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INCF / niQC

NeuroImaging Quality Control (niQC)
https://incf.github.io/niQC/
MIT License
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Project idea: "Knowledge" transfer from "Phantom data analyses"- add scanning "properties" to the model #21

Open yarikoptic opened 3 years ago

yarikoptic commented 3 years ago

Continuing on our "quick" https://f1000research.com/articles/9-1131 publication/finding. I think we should take some published study (or better multiple) with data available, and ideally with a reproducible analysis workflow available and see if addition of such variables as "SAR", "ImageOrientationPatient" which either were extracted/placed into sidecar .json files (or original DICOMs still available and could be extracted) into the model significantly effect the higher-level analyses results of the study.

Those properties are present in DICOMs and often extracted (e.g. if using heudiconv with dcm2niix) and placed into BIDS side car files

a list of openneuro datasets having SAR and/or ImageOrientationPatient ```shell (git)smaug:/mnt/btrfs/datasets/datalad/crawl/openneuro[master]git $> for ds in ds*; do git -C $ds grep -e '"ImageOrientationPatient' -e '"SAR":' -q && echo "- https://openneuro.org/datasets/$ds" ; done ``` - https://openneuro.org/datasets/ds000031 - https://openneuro.org/datasets/ds000113 - https://openneuro.org/datasets/ds000117 - https://openneuro.org/datasets/ds000228 - https://openneuro.org/datasets/ds000249 - https://openneuro.org/datasets/ds000256 - https://openneuro.org/datasets/ds001107 - https://openneuro.org/datasets/ds001241 - https://openneuro.org/datasets/ds001293 - https://openneuro.org/datasets/ds001353 - https://openneuro.org/datasets/ds001399 - https://openneuro.org/datasets/ds001415 - https://openneuro.org/datasets/ds001430 - https://openneuro.org/datasets/ds001439 - https://openneuro.org/datasets/ds001450 - https://openneuro.org/datasets/ds001454 - https://openneuro.org/datasets/ds001461 - https://openneuro.org/datasets/ds001517 - https://openneuro.org/datasets/ds001531 - https://openneuro.org/datasets/ds001545 - https://openneuro.org/datasets/ds001553 - https://openneuro.org/datasets/ds001554 - https://openneuro.org/datasets/ds001555 - https://openneuro.org/datasets/ds001563 - https://openneuro.org/datasets/ds001583 - https://openneuro.org/datasets/ds001600 - https://openneuro.org/datasets/ds001608 - https://openneuro.org/datasets/ds001621 - https://openneuro.org/datasets/ds001645 - https://openneuro.org/datasets/ds001652 - https://openneuro.org/datasets/ds001715 - https://openneuro.org/datasets/ds001722 - https://openneuro.org/datasets/ds001728 - https://openneuro.org/datasets/ds001740 - https://openneuro.org/datasets/ds001747 - https://openneuro.org/datasets/ds001748 - https://openneuro.org/datasets/ds001761 - https://openneuro.org/datasets/ds001762 - https://openneuro.org/datasets/ds001775 - https://openneuro.org/datasets/ds001838 - https://openneuro.org/datasets/ds001840 - https://openneuro.org/datasets/ds001847 - https://openneuro.org/datasets/ds001875 - https://openneuro.org/datasets/ds001919 - https://openneuro.org/datasets/ds001921 - https://openneuro.org/datasets/ds001923 - https://openneuro.org/datasets/ds001942 - https://openneuro.org/datasets/ds001946 - https://openneuro.org/datasets/ds001981 - https://openneuro.org/datasets/ds002011 - https://openneuro.org/datasets/ds002014 - https://openneuro.org/datasets/ds002033 - https://openneuro.org/datasets/ds002040 - https://openneuro.org/datasets/ds002087 - https://openneuro.org/datasets/ds002105 - https://openneuro.org/datasets/ds002116 - https://openneuro.org/datasets/ds002147 - https://openneuro.org/datasets/ds002153 - https://openneuro.org/datasets/ds002155 - https://openneuro.org/datasets/ds002156 - https://openneuro.org/datasets/ds002158 - https://openneuro.org/datasets/ds002168 - https://openneuro.org/datasets/ds002185 - https://openneuro.org/datasets/ds002236 - https://openneuro.org/datasets/ds002241 - https://openneuro.org/datasets/ds002242 - https://openneuro.org/datasets/ds002250 - https://openneuro.org/datasets/ds002274 - https://openneuro.org/datasets/ds002278 - https://openneuro.org/datasets/ds002293 - https://openneuro.org/datasets/ds002294 - https://openneuro.org/datasets/ds002306 - https://openneuro.org/datasets/ds002320 - https://openneuro.org/datasets/ds002328 - https://openneuro.org/datasets/ds002336 - https://openneuro.org/datasets/ds002338 - https://openneuro.org/datasets/ds002345 - https://openneuro.org/datasets/ds002358 - https://openneuro.org/datasets/ds002363 - https://openneuro.org/datasets/ds002367 - https://openneuro.org/datasets/ds002372 - https://openneuro.org/datasets/ds002374 - https://openneuro.org/datasets/ds002393 - https://openneuro.org/datasets/ds002411 - https://openneuro.org/datasets/ds002547 - https://openneuro.org/datasets/ds002574 - https://openneuro.org/datasets/ds002614 - https://openneuro.org/datasets/ds002634 - https://openneuro.org/datasets/ds002655 - https://openneuro.org/datasets/ds002672 - https://openneuro.org/datasets/ds002674 - https://openneuro.org/datasets/ds002683 - https://openneuro.org/datasets/ds002702 - https://openneuro.org/datasets/ds002715 - https://openneuro.org/datasets/ds002717 - https://openneuro.org/datasets/ds002727 - https://openneuro.org/datasets/ds002766 - https://openneuro.org/datasets/ds002773 - https://openneuro.org/datasets/ds002776 - https://openneuro.org/datasets/ds002785 - https://openneuro.org/datasets/ds002790 - https://openneuro.org/datasets/ds002793 - https://openneuro.org/datasets/ds002799 - https://openneuro.org/datasets/ds002809 - https://openneuro.org/datasets/ds002814 - https://openneuro.org/datasets/ds002837 - https://openneuro.org/datasets/ds002842 - https://openneuro.org/datasets/ds002862 - https://openneuro.org/datasets/ds002872 - https://openneuro.org/datasets/ds002873 - https://openneuro.org/datasets/ds002878 - https://openneuro.org/datasets/ds002898 - https://openneuro.org/datasets/ds002900 - https://openneuro.org/datasets/ds002902 - https://openneuro.org/datasets/ds002912 - https://openneuro.org/datasets/ds002938 - https://openneuro.org/datasets/ds002939 - https://openneuro.org/datasets/ds002940 - https://openneuro.org/datasets/ds002982 - https://openneuro.org/datasets/ds002990 - https://openneuro.org/datasets/ds002994 - https://openneuro.org/datasets/ds002995 - https://openneuro.org/datasets/ds003005 - https://openneuro.org/datasets/ds003008 - https://openneuro.org/datasets/ds003011 - https://openneuro.org/datasets/ds003017 - https://openneuro.org/datasets/ds003037 - https://openneuro.org/datasets/ds003098 - https://openneuro.org/datasets/ds003103 - https://openneuro.org/datasets/ds003114 - https://openneuro.org/datasets/ds003126 - https://openneuro.org/datasets/ds003145 - https://openneuro.org/datasets/ds003151 - https://openneuro.org/datasets/ds003171 - https://openneuro.org/datasets/ds003192 - https://openneuro.org/datasets/ds003216 - https://openneuro.org/datasets/ds003242 - https://openneuro.org/datasets/ds003338 - https://openneuro.org/datasets/ds003342 - https://openneuro.org/datasets/ds003346 - https://openneuro.org/datasets/ds003382 - https://openneuro.org/datasets/ds003419 - https://openneuro.org/datasets/ds003433 - https://openneuro.org/datasets/ds003434 - https://openneuro.org/datasets/ds003436 - https://openneuro.org/datasets/ds003438 - https://openneuro.org/datasets/ds003439 - https://openneuro.org/datasets/ds003440 - https://openneuro.org/datasets/ds003441 - https://openneuro.org/datasets/ds003442 - https://openneuro.org/datasets/ds003443 - https://openneuro.org/datasets/ds003444 - https://openneuro.org/datasets/ds003445 - https://openneuro.org/datasets/ds003446 - https://openneuro.org/datasets/ds003452 - https://openneuro.org/datasets/ds003465 - https://openneuro.org/datasets/ds003466 - https://openneuro.org/datasets/ds003470 - https://openneuro.org/datasets/ds003477 - https://openneuro.org/datasets/ds003479 - https://openneuro.org/datasets/ds003481 - https://openneuro.org/datasets/ds003487 - https://openneuro.org/datasets/ds003495 - https://openneuro.org/datasets/ds003511 - https://openneuro.org/datasets/ds003521 - https://openneuro.org/datasets/ds003540 - https://openneuro.org/datasets/ds003558 - https://openneuro.org/datasets/ds003563 - https://openneuro.org/datasets/ds003568 - https://openneuro.org/datasets/ds003574 - https://openneuro.org/datasets/ds003604 - https://openneuro.org/datasets/ds003606 - https://openneuro.org/datasets/ds003612 - https://openneuro.org/datasets/ds003633 - https://openneuro.org/datasets/ds003639 - https://openneuro.org/datasets/ds003642 - https://openneuro.org/datasets/ds003643 - https://openneuro.org/datasets/ds003653 - https://openneuro.org/datasets/ds003658 - https://openneuro.org/datasets/ds003701 - https://openneuro.org/datasets/ds003707 - https://openneuro.org/datasets/ds003714

The simplest kind would be some analysis on anatomical or DWI per subject, so there is just a single input data file at higher level analysis. If it is an fMRI study with multiple runs, those might be incorporated into lower level model only if there is a large number of runs per subject (unlikely), but as for an initial approximation, we could take average in values between all runs for those and introduce them into higher level analysis. After all I expect SAR be comparable, and ImageOrientationPatient nearly the same across runs (if subjects were not taken out from the MRI between runs, and/or FOV was transferred across sequences).

Note: ImageOrientationPatient is likely a correlated with participant demographics (age, weight and gender). If those were not modeled (unlikely) in the study, those might need to be added into the model first. That all also depends on the particulars of the study and its claims. SAR itself might be a correlate of demographics (weight in particular), didn't check...

Based on our results in aforementioned paper, my hypotheses would be

Additional possible observations/points to keep in mind

parteekcoder commented 1 year ago

@yarikoptic hi could please assign me this issue , i would like be part of your GSOC projects this year

yarikoptic commented 1 year ago

I don't think this project will be a part of this GSOC.

parteekcoder commented 1 year ago

Is incf participating in GSoC this year

raamana commented 1 year ago

Hi Parteek, like I said in another issue, please reach out to and confirm with INCF directly. If they are, they would likely refer you to participating mentors/projects, who are often great IMHO. We have no knowledge of their plans.