Dear Freesurfer Experts,
As one of the new freesurfers, I really appreciate the excellent work of authors as well as great support of users' forum.
A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy updating QA tools after the FSv6 release since the QA Tools v1.2 was written for FSv5.3. If so, is it possible to provide an estimated release date please so as to adjust my plan? Thanks for understanding!
In case, it might take a while to release the next QA Tool, may I dare to provide my attempts of code updating of some functions in QA Tools? The following are the brief list of code adapting steps: 1. modified codes for generating file order list in recon_checker; 2. modified codes for matching segment names for instance from DefaultAsegMeans.txt in gparcmean_from_table; 3. adapted default_FOF and default_status_log for FSv6.
After these adaptation, QA Tools ran through and I only encountered some 'syntax error' in terminal for 2 segments, 5th-Ventricle and WM-hypointensities, that I have to ask the experts to guide me through this point if it's of your interests. To ensure the QA Tools functioning well, I tested 116 elderly patients and detected reasonable outliers per patient. Therefore, I would like to double that my code updating based on my general understanding of QA Tool still fit to the basic purpose of authors by asking the following theoretical questions:
1. SNR and segments outliers detection are measures of quality assessment in QA Tools. Have other factors such as subject's motion, image bias, resolution etc. been considered in QA Tools or future release? The default SNR threshold is 16 based on any reference? The max SNR of my patients so far is 32. Any idea of scores of healthy elderly controls?
2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include output of brainstem substructures and HippocampalSubfields of FSv6? If yes, I would like to adapt the codes and provide you some feedback if you think that I can help bit.
3. Future directions mentioned in QA Tools wiki site are interesting and thoughtful. Are other features like 'Detect outliers in aparc and aparc2009 volumes' on the way?
4. Is there a function to summarize all QA measures to csv files, like the quantifyBrainstemStructures.sh in brainstem substructures?
Thank you in advance!
Kind regards,
Yong Li, PhD _________________________ Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany