Derin,
You probably mean the final longitudinal runs (not 'scans'). The longitudinal (-long) runs really should be fine without extra editing. We have never tried editing them as it was never necessary. They should be OK, if not there is likely a problem before that needs to be fixed (e.g. inaccurate registration with the template etc). If that happens, please let us know.
So I went back and checked a few things:
-brainmask is taken from the base, so if it is wrong, check the base -talairach.lta also comes from the base and needs to be checked there -talairach.xfm (only for etiv) is currently taken from the cross sectionals and needs to be checked there. It might be easier to just take the ICV from the base-template instead for all time points, ICV should not change (in adults). - WM edits are merged in from the base (so editing the longitudinal in addition should work, but probably not necessary). - The normalization control points are the only thing I am not really sure about. We played around with several options (copying it from the base, or from the cross sectional). I am not sure what the current mechanism is, maybe the CP go into the long stream indirectly? We'll check and update the WIKI.
Best, 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: 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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