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: mreuter@nmr.mgh.harvard.edu
> To: freesurfer_zg@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
> >
> >
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