Hi Mike, It seems that it usually happens when the surfaces have been rebuilt and the aparc is out of date (and needs to be rebuilt). Can you try
recon-all -make all <subjectID> and see if it rebuilds aparc. If you are still having trouble, please feel free to upload the dataset (details in the wiki). https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Sita. On Tue, 23 Mar 2010, Michael Waskom wrote: > Hi Sita, all, > > I got the rest of the recon to run, made pial edits on the brainmask after > autorecon2, and then reran it to the end. It looks like the reconstruction > of the cortical surfaces and the inflation worked fine, but the cortical > parcellation is totally scrambled. I'm attatching an image of the inflated > left hemisphere with the aparc annotation overlay. (It looks much the same > on the right hemisphere). I'm also attaching the recon-all.log file. Do > you have any idea what might be causing this problem? > > Thanks, > Mike > > On Thu, Mar 18, 2010 at 2:54 PM, Sita Kakunoori > <s...@nmr.mgh.harvard.edu>wrote: > >> >> Hi Mike, >> >> I don't think the motion artifact could've been causing this error. >> It's probably a good idea to fix the talairach if you think it's off >> because if you are reporting the talairach coordinates, you would want the >> talairach transform to be reasonably accurate. >> >> >> Sita. >> >> >> On Thu, 18 Mar 2010, Michael Waskom wrote: >> >> Hi Sita, >>> >>> Running it with the -no-wsgcaatlas seems to do the trick as far as >>> avoiding >>> a segmentation fault. The T1 looks like it has a some motion >>> artifact--might that be causing problems? I checked the Talairach >>> transform >>> and it looks generally alright, although I think it could be improved with >>> some tweaking. It passed the automatic failure detection each time I ran >>> recon-all, though. Would you recommend trying to improve the transform so >>> that things down the line run more smoothly? >>> >>> Best, >>> Mike >>> >>> >>> >>> On Thu, Mar 18, 2010 at 1:22 PM, Sita Kakunoori <s...@nmr.mgh.harvard.edu >>>> wrote: >>> >>> >>>> Hi Mike, >>>> >>>> Did you check the talairach. And how do nu.mgz and T1.mgz look. >>>> Also you could probably try running the following command to see if the >>>> skull strip step finishes without errors. >>>> >>>> recon-all -skullstrip -no-wsgcaatlas -s <subjid> >>>> >>>> Sita. >>>> >>>> >>>> >>>> >>>> On Thu, 18 Mar 2010, Michael Waskom wrote: >>>> >>>> Hi Bruce, Nick, >>>> >>>>> >>>>> I'm getting a segmentation fault that's crashing recon-all at the start >>>>> of >>>>> the watershed during skull-stripping. I've tried this three times, once >>>>> starting the unpacking stream fresh from the raw dicoms, and it keeps >>>>> happening at exactly the same place. I've been reconstructing brains of >>>>> other subjects in the same directory all the while, so I don't think >>>>> it's >>>>> a >>>>> permissions issue of any sort. >>>>> >>>>> Full recon-all log is atatched, but here's the section where it crashes: >>>>> >>>>> *************************WATERSHED************************** >>>>> Sorting... >>>>> first estimation of the COG coord: x=116 y=166 z=95 r=51 >>>>> first estimation of the main basin volume: 585576 voxelsSegmentation >>>>> fault >>>>> Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 >>>>> x86_64 GNU/Linux >>>>> >>>>> recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010 >>>>> >>>>> >>>>> And here's the OS data from the bugr script: >>>>> >>>>> FREESURFER_HOME: /software/Freesurfer/4.4.0 >>>>> >>>>> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 >>>>> >>>>> Debian version: squeeze/sid >>>>> >>>>> Kernel info: Linux 2.6.31-20-generic x86_64 >>>>> >>>>> >>>>> Do you have any idea what might be going wrong? >>>>> >>>>> Thanks! >>>>> Mike >>>>> >>>>> >>>>> >>>> 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
