Hi Mehul, in FS4.5:
- if there are manual CP edits in the cross sectionals, the longitudinal will automatically copy them. - there is a flag (-uselongbasectrlvol) to optionally use the CP from the base (mapped to the current time point) The WM edits are transferred from the base by default, probably we'll do it similar as above in the next release. So yes: WM edits in the base currently. CP in the Cross sectionals, or edit the base and try the flag. The problem with the flag is, that because of atrophy/change, the points might be added into regions that are not WM in a specific longitudinal run. Best, Martin On Mon, 2010-03-15 at 23:44 -0700, Mehul Sampat wrote: > Hi Martin, > > > Just wanted to clarify one question about edits to the longitudinal > pipeline. > > > Lets say there is a data-set with 200 subjects with 5 time-points each > (1000 scans total). > > > I create the base image and i would only like to make corrections in > the 200 base images (if required) and not in the cross-sectional > time-points. My understanding from an earlier thread was that this > should be fine. > > > But in this thread you said control points are copied from the > 'cross-sectional by default' > So is the following correct? > I should only make edits to the wm.mgz (from the base) and avoid > adding any control points to the base ? > > > I apologize for the repeated questions on the issue, but just wanted > to make sure that I was making the corrections correctly. > > > Thanks > Mehul > > On Thu, Mar 11, 2010 at 7:20 PM, Martin Reuter > <mreu...@nmr.mgh.harvard.edu> wrote: > Derin > > OK, Allison discovered it in the depth of recon-all :-) > > The control points are copied from the cross sectional by > default (and > should be edited there). There is an optional flag to get them > from the > base, but that has never been really tested. It only makes > sense if > there is very little structural change across time. But might > save > people some editing time, if they have 10 images with almost > no WM > change. > We'll probably do a similar setup for the WM edits in the next > release. > > Cheers, 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 . 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