Hi Mark,

I talked to Allison and you should be able to rerun 5.1 on top of 5.0 but do NOT use the -clean flag (as it will delete your edits). Just make sure you make a backup copy of your data before doing this.

Another thing: manual edits to the brainmask are treated differently from most manual edits in FreeSurfer and I am not sure exactly what will happen. I believe FreeSurfer keeps the brainmask.mgz if it is already there. This means that edits are kept, but also that your cross sectional analysis will still be biased, as tp1 brainmask was created with 5.0 (and will not be re-created) and tp2 brainmask was created with 5.1. You can recreate brainmask by simply deleting it (and brainfinalsurf and corresponding manedit files if exist) but then you will of course also loose your edits to those files.

Now the good news. The way I implemented skull stripping in the longitudinal stream it uses a union of the cross sectional masks after registration in the base and also for the long runs (same mask for all of them). Thus, it removes the bias in the longitudinal processing. So you should be fine.

Edits is a very complicated topic in the cross sectional processing for historic reasons, and also in longitudinal processing as it inherits some of those problems (but fixes some also :-).

Best, Martin

On Tue, 2012-02-07 at 22:46 -0500, Martin Reuter wrote:

Hi Mark,

So the first thing is you absolutely need to re-run you 1st year data with 5.1 The reason is that you will introduce potential bias by running the different time points with different software (consistently). As a side note: The same is basically true when they do software updates on the scanner which can void a study especially with only two time points.

So the first thing is to figure out how to preserve your edits from 5.0 to 5.1 which should be possible (although I don't know how, maybe Allison or someone else knows)?

Once that is done we will have to look into the edits in the long stream. It will probably depend on the types of edits you have. Some gets transferred automatically and some can be transferred.

Best Martin

On Feb 7, 2012, at 20:44, Mark Fletcher fletche5@illinois.edu wrote:

...

Dear Everyone,

First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream.

I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years data through the recon-all step while using version 5.0. Additionally, I made a substantial amount of corrections to many brain regions that I am hoping to not redo (with the number of subjects in my study it will take well over a month or two to re-do this).

I collected my second years worth of data after 5.1 came out, and ran the recon-all on all of these subjects using version 5.1 of FreeSurfer. Similarly, I have already made corrections to this set of data as well.

My ultimate goal is to now use the longitudinal processing stream. I think I understand the process, however, I am wondering if I need to re-do all of my corrections, or if I can salvage my corrections made from previous versions. I am a little concerned about what the -clean flag might do (will it eliminate my corrections?) Furthermore, while looking at your suggestions of editing errors, it says that you can "save time" because some changes only need to be made to the base. However, in my case, I think re-doing all of the edits will actually cost me much more time. I am willing to scrap all of my work if this is necessary, but I am wondering if there is a work-around.

Sincerely, Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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