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