Oh, I see it would prevent us from getting the aseg.stats file.
That's not good; we want the whole enchilada :-)
Never mind; will follow your previous suggestion and run recon-all all the
way through;
Thanks Doug;
Mehul
On Tue, Jun 4, 2013 at 11:41 AM, Douglas N Greve
wrote:
>
> It would sto
Hi Doug,
Thanks; Will do so.
Also I forgot to mention one thing in the previous email:
for case -autorecon3, also there is:
set DoSegStats = 1; (in recon-all script in 5.3 this is line 5526)
would it help, if "set DoSegStats = 1" was used only in -autorecon3
and not in the
-autorecon2
Hi Doug,
Yes, we see the same error as in msg28047.html; here is the line from my
recon-all.log:
mghRead(/mnt/horizon/stage/HLC//004_151_3106223/WBS/Baseline/Freesurfer/mri/ribbon.mgz,
-1): could not open file
In msg28047.html, Milkos suggested that the issue could be the following
line in re
Could you provide the recon-all.log file?
-Zeke
On 05/30/2013 10:24 AM, Gennan Chen wrote:
> Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz
> will not get created till autorecon3. In V4, that is part of autorecon2
> though.
>
> Gen
>
>
> On Thu, May 30, 2013 at 12:24 AM, M
Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will
not get created till autorecon3. In V4, that is part of autorecon2 though.
Gen
On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat wrote:
> ps: i believe my error is the same as the one in this thread:
>
> http://www.mail-a
ps: i believe my error is the same as the one in this thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html
Mehul
On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat wrote:
> Hi Folks,
> I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
> -notal-check -
Hi Folks,
I am running recon-all with -autorecon1 -autorecon2, -nomotioncor
-notal-check -nonuintensitycor
(this is with fs version 5.3)
it almost runs through but toward the end, when mri_segstats is called I
get the error message:
.../mri/ribbon.mgz, -1): could not open file
any ideas why this
