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
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On Mar 15, 2016, at 1:43 PM, Bruce Fischl fischl@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 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 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.
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