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
