Derin, You probably mean the final longitudinal runs (not 'scans'). The longitudinal (-long) runs really should be fine without extra editing. We have never tried editing them as it was never necessary. They should be OK, if not there is likely a problem before that needs to be fixed (e.g. inaccurate registration with the template etc). If that happens, please let us know.
So I went back and checked a few things: -brainmask is taken from the base, so if it is wrong, check the base -talairach.lta also comes from the base and needs to be checked there -talairach.xfm (only for etiv) is currently taken from the cross sectionals and needs to be checked there. It might be easier to just take the ICV from the base-template instead for all time points, ICV should not change (in adults). - WM edits are merged in from the base (so editing the longitudinal in addition should work, but probably not necessary). - The normalization control points are the only thing I am not really sure about. We played around with several options (copying it from the base, or from the cross sectional). I am not sure what the current mechanism is, maybe the CP go into the long stream indirectly? We'll check and update the WIKI. Best, Martin On Wed, 2010-03-10 at 15:16 -0600, Derin Cobia wrote: > Martin, > > Not to add more to the confusion, but what if the final longitudinal scans > are "not fine" and need some editing. Can they be rerun in the standard way > to incorporate edits (e.g., -autorecon2-cp -autorecon3 ... ), or should > something different be done? Will rerunning these edited long scans in the > standard fashion disrupt them in some way? My hunch is that it won't, but I > want to make sure. Thanks. > > -Derin > > On Mar 10, 2010, at 2:17 PM, Martin Reuter wrote: > > > OK I get it. There was a confusion about adding control points and > > adding new time points. My answer concerns adding new time points, so > > you can ignore it. Do not add any edited results as new time points. > > > > Concerning your question see the discussion on this list from Feb 12 > > that treats exactly this topic. > > > > In short: > > - edit the cross sectionals (you have done that) > > - run the base and edit the base > > - then the longitudinals should be fine > > > > > > Martin > > > > On Wed, 2010-03-10 at 13:08 -0600, Guang Zeng wrote: > >> Hello, Martin, > >> > >> Thanks a lot for your reply, but I am still not very clear about few > >> issues. > >> I think that is because of my unclear description. > >> > >> What happen is: > >> I have two scans which I want to do longitudinal analysis, however, > >> when I finish the > >> cross-sectional analysis, I found the results are not so good because > >> of the low contrast > >> between white matter and gray matter. I added control points to these > >> two scans, rerun them. > >> The results looks much better now, then I go to the longitudinal > >> stream. However, when I load the > >> longitudinal results, I found the kind of problem happens again (lots > >> of no-label region in superior frontal). > >> So I added control points to the longitudinal results directly, and I > >> want rerun them. > >> > >> Based on your reply, I need consider those longitudinal results which > >> I added control points to as new timepoints, > >> rerun them cross-sectionally again, is it correct? > >> > >> Thanks! > >> Guang > >> > >> > >> Here, I just want to add some control points to the FreeSurfer > >> longitudinal results, > >> not new time points. > >> > >>> Subject: Re: [Freesurfer] modification made to longitudinal results > >>> From: mreu...@nmr.mgh.harvard.edu > >>> To: freesurfer...@hotmail.com > >>> CC: freesurfer@nmr.mgh.harvard.edu > >>> Date: Thu, 25 Feb 2010 10:33:36 -0500 > >>> > >>> Hi Guang, > >>> > >>> Depending on what you do you can choose different routes. Note, for > >> both > >>> of these you first need to run the new timepoint cross sectionally > >> (step > >>> 1 in the description > >>> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): > >>> recon-all -all -s newtpid -i path/to/dicom > >>> > >>> Here are the two options once the cross sectional results are there: > >>> > >>> 1. you have only very few timepoints in the base/template so far (2 > >> or > >>> 3). In those cases I would recommend to rerun the base and rerun all > >> the > >>> longitudinals with the new and more accurate base. The commands are > >> on > >>> the Wiki and are the same as usual. > >>> > >>> 2. you have many time points in your base, the additional time point > >> is > >>> not likely to change the base much. In that case you can simply > >> 'patch' > >>> the base without reprocessing and only run a single longitudinal > >> run. > >>> > >>> Let me know if you want to go route 2 because I am writing a script > >> to > >>> patch the base (there are a few files that need to be added so that > >> the > >>> longitudinal run will go through). If there is demand, I will put > >>> priority on this and make it available. > >>> > >>> Best, Martin > >>> > >>> On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote: > >>>> Hi, there, > >>>> > >>>> I need add some control points to the longitudinal results. > >>>> After adding control points, I need rerun it. which command should > >> I > >>>> use? > >>>> > >>>> recon-all -s subj.long.baseid .... > >>>> or > >>>> recon-all -long subj baseid .... > >>>> > >>>> > >>>> Thanks! > >>>> Guang > >>>> > >>>> > >>>> > >> ______________________________________________________________________ > >>>> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. > >> Sign up > >>>> now. > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> > >> > >> ______________________________________________________________________ > >> Hotmail: Powerful Free email with security by Microsoft. Get it now. > > > > _______________________________________________ > > 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
