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:
- 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.
- 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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