Hi Suzan, (sending this also to the FS support list, where these questions fit best, but sometimes I miss emails there).
If edits are necessary or not depends purely on the quality of your data. I.e. old scanners, low contrast, motion artefacts etc. It also depends on the number of subjects. If you want to quantify small changes in only a few subjects, you need to make sure that FS results are clean and correct. If you are running a population study with 30.000 people you cannot do manual edits at all and have to resort to a quality control paradigm. Furthermore, the longitudinal stream additionally benefits from having the subject template (aka “base”). Usually it is sufficient to edit that instead of all time points (e.g. for skullstrip or surface related problems). In short FreeSurfer does not require edits, it allows users to include edits if they like. It is recommended to check results. Never trust any automated tool blindly. Best, Martin > On 22. Oct 2020, at 03:46, Suzan Maleki <suzan.mal...@monash.edu> wrote: > > > Dear Martin, > > The time and effort of the FreeSurfer team is really appreciated. I would be > grateful if you explain to what extent it is necessary to apply manual edits > for longitudinal processing ? > I have read the FS longitudinal tutorial and noticed so many manual edits > need to be done on Cross > Base >Long scans. For example, having two > time-points that are 3 months apart, is it really necessary to do manual > edits for all the individuals ? > I am wondering what are the reasons that necessitate several manual edits for > longitudinal pipeline, considering that FreeSurfer is one of the best > available and commonly used neuroimaging softwares and supposed to be fully > automated. > Also, how much those manual edits will affect the reproducibility of the > processing ? > Thanks a lot for your help, > Kind regards, > Suzan > > -- > Suzan Maleki > PhD Student > > <>Brain, Mind and Society Research Hub > Turner Institute for Brain and Mental Health > School of Psychological Sciences > Monash University > 770 Blackburn Road > Clayton VIC 3800 Australia > > E: suzan.mal...@monash.edu <mailto:suzan.mal...@monash.edu> > W: www.brainmindsociety.com <http://www.brainmindsociety.com/>
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