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 . 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 >
_______________________________________________ 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.
