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 >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> 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 > > > 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
