You can edit just the base if you will only be working with the longitudinal stream. Currently, running the cross-sectional stream is necessary only to get the 'norm.mgz' file, for input to the base subject.
n. On Sun, 2010-02-14 at 14:06 -0800, Mehul Sampat wrote: > Hi Nick (and Martin) > > Could you please clarify if the edits come only from the base or if > they are copied from the cross-sectionals ? > > It would be great if I only had to make edit in the base . > We have 5 timepoints for each subject (each a year apart) and i want > to use the results from the longitudinal pipeline only. > If I did not need to edit the cross-sectional timepoints and if > editing only the base was okay this would be very helpful. > > Martin, do you normally only make edits to base when using the > longitudinal pipeline ? > Thanks > Mehul > > > On Fri, Feb 12, 2010 at 6:01 PM, Martin Reuter > <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Derin, > > this is how I see it: > > The base might need edits and if it does, they should be made. > As you > say, the surfaces of the longitudinal runs are initialized > with the > surface of the base, so, if it is not correct, this will > pollute all > time points. > > Another reason to edit the base is that wm edits (255) and > deletes (1) > are copied from the base to all time points, as you mentioned. > > Usually this should be sufficient, but maybe you need further > edits in a > specific longitudinal run, never happened to me. > > The old longitudinal processing stream really did not have any > cross > sectional runs. Instead of the base they processed TP1 > (introducing a > bias) and copied the edits from there to the longitudinals. We > now copy > it from the base. > > Hope that helps. > > Nick mentioned that edits are copied from the cross > sectionals, but I > think they only come from the base. At least that is what I > think was > done and therefore put it on the wiki. Maybe Nick can verify > what really > goes on in recon-all as he programmed that part? > > It might make sense to edit the cross sectionals anyway > because: > - you then get more reliable cross sectional results (to > compare to > etc). > - the cross sectional asegs are 'fused' (probabilistic > voting), to > initialize the labeling in the longitudinal runs, so more > accuracy in > the cross sectionals cannot hurt. However I never really found > this to > be necessary, but my data was usually high quality. > > Best, Martin > > > On Fri, 2010-02-12 at 13:51 -0600, Derin Cobia wrote: > > > > Bumping this back up to the list. Could someone please > address? > > > > > > To be more concise, during longitudinal processing, where > are wm/gm > > edits made? On the cross-sectional runs, to the base, or on > > the .long. runs themselves? Thanks. > > > > > > -Derin > > > > Begin forwarded message: > > > > > From: Derin Cobia <d-co...@northwestern.edu> > > > > > > Date: February 1, 2010 3:54:46 PM CST > > > > > > To: "freesurfer@nmr.mgh.harvard.edu Help" > > > <freesurfer@nmr.mgh.harvard.edu> > > > > > > Subject: Longitudinal processing clarification > > > > > > > > > (Questions for all, but maybe more directed towards > Martin) > > > > > > > > > I have some questions about manual edits in regard to the > > > longitudinal stream. Based on the current info on the > wiki page, it > > > appears that no edits are pushed forward from the > cross-sectional > > > (initial) runs of the subject data, as any information on > > > the *.long.* runs come from the template. However, I've > noticed > > > that WM edits and surfs from the template are used for the > *.long.* > > > processing. In essence, my question is when/where should > manual > > > edits (i.e., control points, WM, pial edits) occur when > conducting > > > longitudinal processing in 4.5? It seems I remember that > in 4.3 > > > edits in the cross-sectional work would be pushed forward > to the > > > *.long.* images, but such is not the case anymore (?). > Are edits to > > > occur in the template (i.e., 'base') now, or in the > *.long.* runs? > > > Thanks. > > > > > > > > > -Derin > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
