why are you deleting voxels from the brainmask.mgz? That is only used for
masking out non-brain tissue. Is that what you are trying to do?
On Tue, 15 Mar 2016, Champe Barton wrote:
I used the recon editing tool—I explicitly followed the instructions from the
tutorial (even on reprocessing the tutorial data it didn't work), so I had the
brainmask.mgz highlighted, checked the recon editing box and held shift and
clicked to remove the necessary voxels (they turned black). I removed them on
all the necessary slices as well.
Champe
Sent from my iPhone
On Mar 15, 2016, at 1:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Champe
it must be in the tmp subdirectory (that is <subject name>/tmp/control.dat)
otherwise we will not find it.
As for the deleted voxel issue - how did you delete them?
Bruce
On Tue, 15 Mar 2016, Champe Barton wrote:
I created them as instructed in the tutorial and called the file “control.dat”
so there’s a control.dat file in my subjects directory. Should I have named it
tmp/control.dat? Also, would resolving the control points issue also resolve
the deleted voxels issue? Cause my it’s not redrawing the pial surface either.
Thanks
Champe
On Mar 15, 2016, at 1:22 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
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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