Hi Donald, I have a paper almost published on the longitudinal stream including several repeatability measures (although not everything that you ask for). Let me know if you want to take a peek at it before it goes out. I might be able to send a pre-print version.
Best, Martin On Tue, 2011-12-20 at 11:37 +0800, Thomas Yeo wrote: > Hi Donald, > > With regards to longitudinal analysis, I am not as familiar with the > issue you are mentioning. Perhaps some other person on the list can > comment. > > With regards to your other comments, I think your reading is correct. > However, I should mention that the reported accuracies *really* > depends on what structures (cytoarchitectural areas versus functional > areas versus macro-anatomical areas) and what accuracy measures (e.g., > volume of structures versus overlap of structures, etc.) you are > looking at. You probably already know this, but I will elaborate > anyhow: > > The references by Fischl, Hinds, Yeo (from the previous email) are > talking about the accuracy of localizing cortical cytoarchitectural > and functional areas. Since freesurfer (and most other software > packages) uses macro-anatomy (e.g., sulci, gyri, MR intensity) for > processing (e.g, alignment of subjects, segmentation) and > macro-anatomy does not predict function/cytoarchitecture completely, > we expect the accuracy for cytoarchitectural and functional areas to > be bounded by the predictive relationship between macro-anatomy and > function/cytoarchitecture. In particular, V1 turns out to be very > well-predicted by the cortical folds (calcarine), and so when we align > sulci/gyri across subjects, there's very small errors in localizing > the boundaries of V1. On the other hand, MT turns out to be not as > well predicted by the cortical folds, thus the accuracy of MT > alignment after freesurfer processing is lower. > > Conversely, for macroanatomical structures (stuff that is visibly seen > in MR) like superior temporal sulcus and the thalamus (in aparc+aseg), > we expect the accuracy to be much higher. Even then the accuracy for > individual structures may vary. For example, thalamus is more > accurately segmented than the amygdala. For individual thalamic > nuclei, which are less visible (if not invisible!) in 3T MR, the > accuracy is probably much less. > > You also mentioned that some areas would be larger than the true > underlying labels for certain individuals, and some would be smaller. > That is certainly the case, but I don't think it is explicitly shown > in the papers by Fischl, Hinds, Yeo (although you can probably infer > that from other papers listed in the links I sent you). As an extreme > example, in one of the experiments in Yeo et al. 2010, "ground truth" > functional MT+ for each subject was defined by thresholding the fMRI > activation map using a size threshold. Therefore, the way the "ground > truth" was set up in that particular experiment, any errors in > predicted MT+ is due to errors in predicting MT+ location, rather than > size difference. On the other hand, if you look at Figure 3 in Fischl > et al, 2002 (Whole Brain Segmentation: Automated Labeling of > Neuroanatomical Structures in the Human Brain), there is no obvious > systemic differences between volumetric measurement of structures > obtained by manual labeling versus automated segmentation in > FreeSurfer (circa 2002). > > --Thomas > > > On Tue, Dec 20, 2011 at 2:05 AM, MCLAREN, Donald > <mclaren.don...@gmail.com> wrote: > > Excellent references. From my reading of these papers, the boundaries of an > > individuals subject can shift by up to ~7mm. Meaning that some areas would > > be largers than the standard labels and others would be smaller. > > > > Is my reading of this correct? > > > > In longitudinal analysis of regional volume measures, do you know of anyway > > to correct for the potential correlation induced by the mislabelling of > > nodes that go into each regional volume? > > > > > > Best Regards, Donald McLaren > > ================= > > D.G. McLaren, Ph.D. > > Postdoctoral Research Fellow, GRECC, Bedford VA > > Research Fellow, Department of Neurology, Massachusetts General Hospital and > > Harvard Medical School > > Office: (773) 406-2464 > > ===================== > > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > > intended only for the use of the individual or entity named above. If the > > reader of the e-mail is not the intended recipient or the employee or agent > > responsible for delivering it to the intended recipient, you are hereby > > notified that you are in possession of confidential and privileged > > information. Any unauthorized use, disclosure, copying or the taking of any > > action in reliance on the contents of this information is strictly > > prohibited and may be unlawful. If you have received this e-mail > > unintentionally, please immediately notify the sender via telephone at (773) > > 406-2464 or email. > > > > > > > > On Sat, Dec 17, 2011 at 9:28 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote: > >> > >> There's some reference of test-retest reliability here: > >> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, > >> although I doubt it's complete. There's also a section on the wiki of > >> paper evaluating freesurfer: > >> http://surfer.nmr.mgh.harvard.edu/fswiki/#Articles.evaluations > >> > >> What I know off hand is that for cytoarchitectonics and some function > >> (like MT+ and V1), freesurfer registration accuracy ranges from 2-3mm > >> (V1) to 6-12mm (BA44, BA45, MT+). BA2, BA6, etc in between. Here's the > >> references: > >> > >> Fischl et al. 2008 Cortical folding patterns and predicting > >> cytoarchitecture > >> Hinds et al. 2008 Accurate prediction of V1 location from cortical > >> folds in a surface coordinate system > >> Yeo et al. 2008 Spherical Demons: Fast Diffeomorphic Landmark-Free > >> Surface Registration > >> Yeo et al. 2010 Learning Task-Optimal Registration Cost Functions for > >> Localizing Cytoarchitecture and Function in the Cerebral Cortex > >> > >> --Thomas > >> > >> On Sat, Dec 17, 2011 at 5:49 AM, MCLAREN, Donald > >> <mclaren.don...@gmail.com> wrote: > >> > I've looked through a number of freesurfer papers, but haven't been able > >> > to > >> > find the answer to what I am looking for and was hoping someone had the > >> > references easily available. > >> > > >> > (1) What is the reliability of regional volumes generated from > >> > freesurfer > >> > over time? > >> > > >> > (2) What is the accuracy of labels for these volumes from subject to > >> > subject > >> > (e.g. how close are the freesurfer labels to cytoarchitecture or > >> > manually > >> > drawing the labels)? > >> > > >> > > >> > Best Regards, Donald McLaren > >> > ================= > >> > D.G. McLaren, Ph.D. > >> > Postdoctoral Research Fellow, GRECC, Bedford VA > >> > Research Fellow, Department of Neurology, Massachusetts General Hospital > >> > and > >> > Harvard Medical School > >> > Office: (773) 406-2464 > >> > ===================== > >> > This e-mail contains CONFIDENTIAL INFORMATION which may contain > >> > PROTECTED > >> > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > >> > intended only for the use of the individual or entity named above. If > >> > the > >> > reader of the e-mail is not the intended recipient or the employee or > >> > agent > >> > responsible for delivering it to the intended recipient, you are hereby > >> > notified that you are in possession of confidential and privileged > >> > information. Any unauthorized use, disclosure, copying or the taking of > >> > any > >> > action in reliance on the contents of this information is strictly > >> > prohibited and may be unlawful. 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