not sure it will fix your problem, but worth trying. Zeke: can you get Vy a
new version of mri_mask and mris_make_surfaces. Vy: try out mri_mask first
before replacing mris_make_surfaces as it's a bigger and far less tested
change
On Mon, 1 Apr 2013, Vy Dinh wrote:
Hi Bruce,
I just noticed
Hi Bruce,
I just noticed this reply. Looks like you came to save the day!
I am using a Mac OSX - Snow Leopard 10.6.8
(2 x 3 GHz Quad-Core Intel Xeon)
Thanks,
Vy
On Mon, Apr 1, 2013 at 4:17 PM, Bruce Fischl wrote:
> Hi Vy and Martin
>
> there was a bug in mri_mask that I just fixed that cause
Hi Martin,
Thank you for getting back to me. To clarify what I did:
1. edited all cross-sectionals & reran until surfaces are accurate.
2. created the base from the cross-sectionals.
3. edited base & reran until surfaces are accurate
4. created longitudinal files from edited cross-sectionals & ba
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 prob
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 Re
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
Was wondering if anyone from the Freesurfer team is looking into this issue
yet.
On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh 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 wrote:
>
>> Dear Developers
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 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
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 scan
