Dear Freesurfer Experts, Please excuse my long email yesterday.
Now, I finished code update of the outlier detection part for brainstem substructures (bs) and Hippocampal Subfields (hc) modules. Code updated in the similar way as my last email except that I combined the output of both modules to simplify the process. The following log files might show some clue of my exploration: YongbshcLUT (like asegLUT_112511): Medulla 0.287988 +/- 0.0304379 Pons 0.864817 +/- 0.128019 SCP 0.0161611 +/- 0.0030778 Midbrain 0.388938 +/- 0.038842 Whole_brainstem 1.8246 +/- 0.184472 Left-Hippocampal_tail 0.0291617 +/- 0.00437039 Left-subiculum 0.0237801 +/- 0.0044348 Left-CA1 0.0387709 +/- 0.00612168 Left-hippocampal-fissure 0.00944849 +/- 0.00188347 Left-presubiculum 0.0177329 +/- 0.00272706 Left-parasubiculum 0.00372024 +/- 0.000876862 Left-molecular_layer_HP 0.0320802 +/- 0.00806223 Left-GC-ML-DG 0.0186971 +/- 0.00308382 Left-CA3 0.0120106 +/- 0.00198279 Left-CA4 0.0132618 +/- 0.00261687 Left-fimbria 0.00371701 +/- 0.00166146 Left-HATA 0.0031189 +/- 0.000692806 Left-Whole_hippocampus 0.190022 +/- 0.0246413 Right-Hippocampal_tail 0.030817 +/- 0.00496078 Right-subiculum 0.0248689 +/- 0.00427691 Right-CA1 0.0370719 +/- 0.00873442 Right-hippocampal-fissure 0.0103329 +/- 0.00187117 Right-presubiculum 0.0178487 +/- 0.00260947 Right-parasubiculum 0.00380418 +/- 0.000861778 Right-molecular_layer_HP 0.032938 +/- 0.00448073 Right-GC-ML-DG 0.0168729 +/- 0.00304788 Right-CA3 0.0130893 +/- 0.00239818 Right-CA4 0.0143492 +/- 0.00281808 Right-fimbria 0.00438099 +/- 0.00176098 Right-HATA 0.00338842 +/- 0.0006037 Right-Whole_hippocampus 0.198797 +/- 0.0243668 an example subject's bshc.stats (like aseg.stats): Medulla 4288.386728 Pons 12836.783824 SCP 194.446727 Midbrain 8306.988464 Whole_brainstem 22293.878740 Left-Hippocampal_tail 462.086606 Left-subiculum 307.970217 Left-CA1 816.878818 Left-hippocampal-fissure 118.986208 Left-presubiculum 227.392060 Left-parasubiculum 84.381831 Left-molecular_layer_HP 841.496111 Left-GC-ML-DG 238.308049 Left-CA3 183.383724 Left-CA4 196.098618 Left-fimbria 73.990998 Left-HATA 36.237082 Left-Whole_hippocampus 2838.187477 Right-Hippocampal_tail 408.832729 Right-subiculum 388.667888 Right-CA1 801.601831 Right-hippocampal-fissure 132.071091 Right-presubiculum 242.179137 Right-parasubiculum 43.414171 Right-molecular_layer_HP 487.298072 Right-GC-ML-DG 246.283617 Right-CA3 164.849646 Right-CA4 209.108368 Right-fimbria 90.291400 Right-HATA 42.073898 Right-Whole_hippocampus 2791.300419 icv.txt (actually eITV instead of ICV): 1420463.178113 bshc_outliers.log: Subject 008 Right-HATA value .002080900 is an outlier ... Note: all data here are kind of simulation results because of data safety reason and these logs only serve as signs of correct code update. I guess that both the only output of bs and hc (bshc.stats) is segment volume, not the 'normMean normStdDev ...' in aseg.stats. So is it senseful to include those 'norm*' measures in the bs & hc modules in the future? BTW, is there an advantage to use normMax / eITV rather than normMean / eITV in outlier detection in theory? Thank you very much again! I wish all of you a nice weekend! Best regards, Yong _________________________ Yong Li, PhD Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany On Thu, Apr 6, 2017 at 11:36 AM, Yong Li <yongl...@gmail.com> wrote: > 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 > > > > > > >
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