Great! Thanks! Mihaela On Thu, May 28, 2015 at 12:36 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu > wrote:
> Hi Mihaela, > > it should still work, but may require more edits than with adults (e.g. if > head size changes, the skull strip may differ a lot across time points. We > keep it fixed in the base by computing the union, but that may be too > large for some earlier time points, so you may have to edit them in the > long etc.). > > Best, Martin > > > On 05/28/2015 11:54 AM, Mihaela Stefan wrote: > > Dear Martin, > > I'm pitching in since this topic concerns me as well. > We are collecting structural data for a longitudinal study with > adolescents. The youngest is 13 years old at baseline and the mean age is > around 16. We will collect 3 follow-ups with a gap of 1.5 - 2 years. The > adolescent brain is still in the process of growing but not that > dramatically as at 4. > Can we use the longitudinal stream? > > Thanks! > Mihaela > > On Thu, May 28, 2015 at 11:13 AM, Clara Kühn <cku...@cbs.mpg.de> wrote: > >> Hi Martin, >> >> thanks for your quick reply. I was indeed referring to the quality check. >> I guess I interpreted that incorrectly. With the children data "inspecting" >> almost always means "editing". >> >> I also took a look at the cheat sheet again. I've been mulling it over >> and my best idea so far is to >> >> 1. check/ edit the crosses for control points and rerun autorecon2-cp >> -autorecon3 since those get transferred to the long directly >> 2. check the base and edit the brainmask (eg taking out blood vessels and >> tentoral membrane or cloning voxels if necessary) since it gets transferred >> to the long directly >> 3. check the base and edit the wm mask and rerun -autorecon2-wm >> -autorecon3 in the base command >> 4. check the longs and hope everything is fine :) >> >> We measured the 4 year olds with a gap of 3 weeks between scans with the >> assumption that their heads won't grow considerably within 2 months time. >> What do you think? >> Cheers, Clara >> >> ----- Ursprüngliche Mail ----- >> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu> >> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> >> Gesendet: Donnerstag, 28. Mai 2015 16:45:57 >> Betreff: Re: [Freesurfer] what order for longitudinal edits >> >> Hi Clara, >> >> how to edit depends a lot on the type of edit. The general rule is to >> edit as early as possible. In some edits, there is shortcuts (e.g. start >> with base, then check long and skip the cross). Take a look at the Cheat >> Sheet on the first link. Also usually there is no need at all to edit >> the longs, as the edits in cross and base should fix everything >> sufficiently. So in the case of a shortcut (editing base, skipping >> cross) you only need to edit 1 run (the base) per subject, not all 3 >> time points. >> >> I also cannot find the contradiction in the first page. Where does it >> say to start editing with the longs, then go backwards? That would >> certainly be wrong for editing. Can you please point me to that, so I >> can fix it (if it is there). Maybe you confused this with QC (quality >> check) which you could do backwards to save time. E.g. if the longs are >> look great, no need to check base and cross. >> >> "QC from back to front (long -> base -> cross), once you find where >> problems occur, edit from front to back (cross -> base -> long)." >> >> Cheers, Martin >> >> P.S. probably more important, I doubt that the longitudinal stream will >> work well on 4-year olds. The basic assumption is that head size does >> not change, so if that is approximately true, it could work (e.g. short >> time intervals). Otherwise you may run into lot's of editing problems >> and it may be easier to just use the cross sectionals in your analysis >> (at the cost of increased measurement variability). >> >> >> On 05/28/2015 10:19 AM, Clara Kühn wrote: >> > Dear Freesurfer Experts, >> > >> > I'm working with the structural data of 4-year olds which we measured 3 >> times to asses changes in cortical thickness. >> > During the preprocessing I've found some contradicting information on >> how to best edit the longitudinal data. On this site >> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it says to >> edit stuff as early as possible. However, on the same site it says to start >> with the longs, then the base and then the cross. And on this site >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#FsTutorial.2BAC8-LongitudinalTutorialfreeview.EditingLongitudinalData >> it says to check the base first and then the longs. >> > I am utterly confused as to how I can edit my data most efficiently >> because I have a lot of it (100 children, 3 scans each). >> > >> > To me, it is also unclear at which point I can edit the long and rerun >> the recon process partially (eg. with the -wm flag) and when it is >> necessary to go back to the base... >> > >> > I am very thankful for any kind of revelation on these matters :) >> > Cheers, >> > Clara Kühn >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> -- >> Dr. Martin Reuter >> >> 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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Dr. Martin Reuter > > 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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