Hi Joy-Loi, yes, you can do that using the free surfer tools (e.g. check if 'atrophy', i.e. change across the two methods, is different from zero, meaning if there is a bias).
Any of the statistical methods described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics can do that. You will find that results differ, but you will not know if they differ because of the - different quality of the scans - difference in processing (averaging 2 scans) - or simply the noise one would always expect from the scanner (imaging / positioning etc). It would be interesting to distinguish those sources of variability. But for that you'd need a second time point I think. Best, Martin On Mar 19, 2013, at 10:47 AM, Joy-Loi Chepkoech <[email protected]> wrote: > Hello Martin, > > Thank you for your swift reply. > > I failed to make myself clear, and will try describing my study again. First, > an important point: the study is not longitudinal per se, but I am interested > in applying the methods of longitudinal analysis. I only have one time point, > all the scans have been collected within the same session. > > I am studying a large group of subjects whom each underwent a scan session > with 4 scans. Each of these scans were graded for quality on a scale from 1-4. > An example of what I then did was to process each subject twice, once with > the scan of quality ”1”, and a second time averaging the scans of quality ”1” > and ”2”, thus resulting in two groups between which each subject is compared > to itself. > > Now I am attempting to set up a longitudinal analysis with this data. I have > processed through the longitudinal stream, and I guess my question starts at > the point of post-processing: How, if feasible, can I transfer the idea of > “across group comparison between time point and time point 2” to “across > group comparison between 1 scan and 2 scans” in setting up the QDEC table and > continuing from there? > > I hope this make sense, your help is greatly appreciated. > > Best regards, > > Joy-Loi > > > > > > On 2013-03-18 19:13, Martin Reuter wrote: >> Hi Joy-Loi, >> so you have 2 time points? the first with a single scan, the second >> with two within-session scans that you want to average? I don't >> understand exactly what you are trying to do. To test differences in >> reliability you'd have to scan a bunch of subjects twice in a session >> and then twice in another session. >> Then you can look at reliability when using only one scan (e.g. the >> first) or when averaging both scans in both time points. 'varying >> quality' with respect to motion also scares me a little. There can be >> individual outliers that severely affect your mean response (unless >> you have lots of subjects). >> Anyway for these things you would process your results through the >> longitudinal stream (this allows you also to be unbiased with respect >> to the time point). There are several design questions to consider >> (e.g. does it make sense to include all virtual time points into the >> same base, or run everything twice: one base for the averaged images , >> another for the single images and then compare etc. ) Either way this >> is not a standard analysis and you'd be pretty much on your own with >> how to set it up. >> Best, Martin >> On 03/18/2013 09:02 AM, Joy-Loi Chepkoech wrote: >>> Hello FreeSurfer experts, >>> I am currently trying to systematically investigate the differences in >>> cortical and subcortical estimates that occur when performing recon-all >>> on one scan, or when averaging across scans of varying quality with >>> regard to movement. >>> I have a list of subjects that each have been processed (recon-all) >>> twice (once with one scan and once with two scans), and would like to >>> run some FreeSurfer statistical analysis on them. >>> Is it feasible to set up a longitudinal analysis similar to the one >>> described here: >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)? >>> If it is, could someone assist me in setting this analysis up? >>> (I have tried following the tutorial, where I on each subject set "0 >>> years" for one scan, and "1 year" for two scans in the QDEC table, but >>> the results from the QDEC analysis don't seem to agree with previous >>> SPSS results that I have). >>> Thank you, >>> Joy-Loi >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Dr. Martin Reuter >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> Phone: +1-617-724-5652 >> Email: >> [email protected] >> [email protected] >> Web : http://reuter.mit.edu >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: [email protected] [email protected] Web : http://reuter.mit.edu
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