Hi Martin, Wasn't sure whether you'd seen my reply below, look forward to hear back your thoughts, thanks! Tudor On 25 May 2014 21:40, "Tudor Popescu" <tud...@gmail.com> wrote:
> Thanks very much Martin and Bruce. I guess I'd misread the Wiki (my own > fault, not the text's), and am glad to hear that the longitudinal pipeline > is in fact perfectly suitable for my needs here. > > Having run the first 2 steps (cross and base), I'm a bit unclear how the > output so far has to be manually inspected. It says in the tutorial > <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial> that you > should load each subject's base volume + surfs in freeview and then "move > back and forth a few slices". However, even just loading each base in this > manner takes ~1 min on my PC (CoreDuo, 4GB, Ubuntu Virtualbox in Windows > 7), and then moving with PgUp/PgDn between all coronal slices (starting > from the default slice=128, going all the way posterior and then all the > way anterior) is excruciatingly slow. All of this would have to be repeated > for all my 72 subjects - is there any way to optimise this manual > inspection? > > Also, if the surfs turn out to not follow the volume correctly, presumably > the thing to do is white surface correction + re-running recon. But what > should one do if, due to an erroneous averaging between timepoints, you see > blurs/ghosts in your base template? > > Many thanks! > Tudor > > > On 9 May 2014 21:33, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Tudor, >> >> the longitudinal pipeline in FS is actually one of the best on the planet >> as far as I know :-). If there is any contradictory information on the >> wiki, can you point me to that so I can see what causes the misconception. >> Really: compared to independent processing, it significantly increases >> sensitivity. Also we have designed it to be unbiased with respect to a >> single time point or directionality. It is quite mature by now. >> >> You should definitely use the longitudinal pipeline for the analysis of >> your data. Now to your questions >> >> 1. QDEC: I am not too familiar with qdec. You can definitely try the >> 2-stage approach described on the wiki. There you first compute a measure >> of change (e.g. hippocampal volume change during your week) and then >> compare that measure across groups similar to a cross sectional >> volume/thickness analysis. You can also use our tools to run a linear mixed >> effects model if you want to do that (it is more involved and requires you >> to use matlab tools). In your case, you probably have 2 time points for all >> subjects and the time distance is probably the same for all subjects, so >> the 2-stage approach should be fine. >> >> 2. The image processing is done via the longitudinal pipeline (three >> steps: cross, base, long), to prepare the data look at the description of >> the 2-stage model >> http://freesurfer.net/fswiki/LongitudinalTwoStageModel >> and also the longitudinal tutorial >> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial >> >> 3. At the recon all level in FS you get (after the 3 steps) measurement >> for all time points. So you would compare those results across time in the >> stats. >> >> Hope that helps, Martin >> >> >> On 05/08/2014 08:14 AM, Tudor Popescu wrote: >> >> Sorry for the repeat, wasn't sure whether this was received the first >> time. >> Tudor >> >> >> On 6 May 2014 19:55, Tudor Popescu <tud...@gmail.com> wrote: >> >>> Dear FS list, >>> >>> I have structural data from a learning study (pre&post-training scans, >>> with 3 groups). Although the training was only one week, I'm guessing from >>> an analysis point of view, this still qualifies as longitudinal. I want to >>> check for >>> >>> - the main within-subjects effect of time point (pre&post) >>> - the main between-subjects effect of group (treatment A, treatment >>> B, control), >>> - the time x group interaction >>> >>> I intend to look at thickness, surface area, volume, and lGI. >>> >>> I read on the wiki >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing> that >>> FS is currently not optimal for longitudinal analyses. I intend my >>> FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is >>> in fact a good idea to do this, my questions (not covered in the >>> 'longitudinal' wiki page) are: >>> >>> 1) Can QDEC be used for such an analysis, and if so, what would be >>> different as compared to a cross-sectional (no temporal/within factor) >>> study? >>> >>> 2) Also, is the pre-processing stage any different? >>> >>> 3) In FSL, for longitudinal designs you do stats on images obtained as >>> the difference between consecutive time points. Does this have to be done >>> in FreeSurfer as well, and if so, is it done at the recon-all level or only >>> at the stats (QDEC) level? >>> >>> Thanks! >>> >>> Tudor >>> >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Martin Reuter, Ph.D. >> >> Instructor in Neurology >> Harvard Medical School >> Assistant in Neuroscience >> Dept. of Radiology, Massachusetts General Hospital >> Dept. of Neurology, Massachusetts General Hospital >> Research Affiliate >> Computer Science and Artificial Intelligence Lab, >> Dept. of Electrical Engineering and Computer Science, >> Massachusetts Institute of Technology >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreu...@nmr.mgh.harvard.edu >> reu...@mit.edu >> Web : http://reuter.mit.edu >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> >> >
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