p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton
wrote:
Hey Bruce,
I recently sent you a log file to look at to determine why reprocessing data
wasn’t making any changes in freeview. Have you had a chance to go over it yet?
Let me know.
Thanks,
Champe
On Mar 7, 2016, at 11:41 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:
Hey Bruce,
I got a notification saying the email my recon-all.log file attachment was too
large and had to await moderator approval to be posted to the support list. I
was just wondering if you received it or if I should resend it.
Best,
Champe
Sent from my iPhone
On Mar 6, 2016, at 9:53 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Champe
can you send us the recon-all.log file?
cheers
Bruce
On Sun, 6 Mar 2016, Champe Barton wrote:
Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid <my subject ID>, it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?
And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.
Thanks,
Champe
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