Hi Vy and Martin

there was a bug in mri_mask that I just fixed that caused the
brain.finalsurfs.mgz to be empty when the brain.finalsurfs.manedit.mgz
existed. Vy: if you tell us what hardware/software platform you are using
we can get you an updated version. Not sure if this will fix your problem,
but it might. I also modified mris_make_surfaces in a way that could help
and you can try a new version of that if mri_mask doesn't fix things for
you

cheers
Bruce

On Mon, 1 Apr 2013, Martin Reuter wrote:

>
> Also: brain.finalsurfs.manedit is mainly for correcting situations where the
> pial surface extends into the cerebellum. Did that happen in your case
> without editing? For other edits (e.g. pial including dura) you should fix
> the brainmask.mgz .
>
> Best, Martin
>
>
>
> On 04/01/2013 04:39 PM, Martin Reuter wrote:
>       Hi Vy,
>
>       not sure what it going on in your data. Surfaces are copied from
>       the base and if they are not accurate there you need to fix it
>       there. It seems you did that and you worked the edits in the
>       right order.
>
>       What exactly happened? You fixed cross and base and everything
>       look fine. When you run long it looks fine, but when you edit
>       long and run it again it messes up?
>
>       Did you edit only the brain.finalsurfs or also other things at
>       the same time? Also, if you edited long, these edits will be
>       kept and not replaced with new edits from base or cross. So if
>       cross or base get edited it may be good to rename or remove the
>       edit file in the long and run long without edits again. This way
>       the cross and base edits get transferred to long automatically.
>       Only if that is not sufficient you need to do edits in the long.
>
>       Sorry I cannot say more right now without knowing what you did.
>
>       Best, Martin
>
>
>

>             On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh
>             <vy_dinh@rush.edu> wrote:
>                   BTW, we are using Freesurfer 5.1:
>                   freesurfer-i686-apple-darwin9.8.0-stable5-20110525
>
>                   On Fri, Mar 29, 2013 at 10:08 AM, Vy
>                   Dinh <vy_dinh@rush.edu> wrote:
>                         Dear Developers, 
> I have a significant problem when rerunning the pial
> edits for the longitudinal data. Our dataset
> consists of subjects & a followup scan (for each
> sub). To be thorough, we edited
> brain.finalsurfs.manedit.mgz (as it was further in
> the processing stream) for the cross-sectional
> scans, the base scans, and the longitudinal scans.
> The longitudinal data were created only after the
> base has been edited and rerun. Likewise, the base
> was only created and rerun after the
> cross-sectionals were finalized. 
>
> We work with a clinical population so minor edits do
> show up on the longitudinal scans. However, after
> editing and recreating the surfaces from these
> longitudinal scans, the pial surfaces has extended
> to include dura & other voxels that were not
> previously included within the pial surface (during
> the initial creation of the longitudinal data). We
> tried both commands (listed below) and get this same
> problem:
>
> recon-all -autorecon2-pial -autorecon3 -long tpN
> tp_base
> (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits)
> or recon-all -autorecon3-pial -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)
>
> Could you please help us figure out why the pial
> surface extends to include nonbrain regions when
> recreating the surfaces? 
>
> What solutions would you suggest in resolving this
> problem?
>
> Thank you,
>
> Vy Dinh
> Research Associate
> Department of Neurological Sciences 
> Rush University Medical Center
>
>
>
>
>

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