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 >>>>>>> _______________________________________________ >>>>>>> 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. 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