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 fischl@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 fischl@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 fischl@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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