Hi Clara, this sounds great. The short time distance between the scans should also help, so I think there is a good change it will work like this. good luck, Martin
On 05/28/2015 11:13 AM, Clara Kühn 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. 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