Hi Rashimi, please read http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it should explain everything.
The clean way would be to edit the brainmask in the cross sectional runs, complete them, run the base and the longs. Optimally no edits should be necessary in the base and longs if cross are correct. A potential short cut (depending on how bad the skull strips are) would be to run cross and base, then edit only the base. This can work if the skull strip is not too bad and if the asegs in the cross are good. Best, Martin. On Thu, 2012-09-27 at 16:04 +0000, Rashmi Singh wrote: > Hello FreeSurfer expets, > Our study requires our subjects to be scanned 3-4 times and then I use > FreeSurfer Tool to generate their voulumetrics. Since I do several time > points on a subjects also perform the longitudinal runs and then take the > volumetrics information from longitudinal run output for each time point > subject wise. > To do the ccros sectional time point runs I performed run recon all on my > subjects T1 Mparge data as follows: > recon-all -s SUBjid -use-mritotal -all </dev/null&> outFSSubjid & > > I examined the output data for skull stripping and I am finding errors. > What do you suggest: shall I try to correct the skull stripping on the > cross sectional out put before performing the base and longitudinal run or > shall I complete all the runs and do skull strip editing in the output of > the longitudinal run data. > Please advise. > Thanks, > Rashmi. > > > I am > > On 3/2/12 8:02 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > >Hi Rashmi > > > >what version of FS are you using? And what sequence are you using? There > >will of course be noise-induced variation across scans, which in the best > >case is around 2%. But that only occurs if you use multi-echo (high > >bandwidth sequence) and are careful about subject positioning to minimize > >differential gradient nonlinearity distortions. You should also make > >sure > >that your outlier measurements aren't significantly more motion corrupted > >than your other scans. Finally, it can also help to control for hydration > >status and time-of-day. > > > >cheers > >Bruce > > > > > > > >On Thu, 1 Mar 2012, Rashmi Singh wrote: > > > >> Hello, > >> I am finding differences in hippocampus voulme of same subject when > >>scanned at different times . Our study requires our subjects to be > >>scanned 3-4 times (T0-T3) within a > >> period of 1 month. We have performed MRI Scanning on all our subjects > >>with same sequence using 3T GE scanner. > >> Please suggest the reason behind this difference and how would I go > >>about correcting it. > >> For example following are the hippocampal values for two subjects ( A > >>and AA ) calculated by freesurfer from different scans. Surprisingly > >>for these two subjects T3 and T2 > >> Hipp-values for A and AA respectively that are differing from the > >>other timepoints are same. > >> > >> Left-Hippocampus > >> Right-Hippocampus > >> A.T0 > >> 3537 > >> 3632 > >> A.T1 > >> 3629 > >> 3796 > >> A.T2 > >> 3536 > >> 3782 > >> A.T3 > >> 3096 > >> 3671 > >> AA.T1 > >> 4245 > >> 4667 > >> AA.T2 > >> 3096 > >> 3671 > >> AA.T3 > >> 4341 > >> 4491 > >> > >> > >>_________________________________________________________________________ > >>_________________________________________________________________________ > >>______________________________ > >> > >> This document may contain information covered under the Privacy Act, 5 > >>USC 552(a), and/or the Health Insurance Portability and Accountability > >>Act (PL 104-191) and its various > >> implementing regulations and must be protected in accordance with those > >>provisions. Healthcare information is personal and sensitive and must be > >>treated accordingly. 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