There should be a -s before the subjectID. So the command line is recon-all -make all -s <subjectID>
Thanks, Sita. On Wed, 24 Mar 2010, Sita Kakunoori wrote: > > 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 the aparc is out of date (and needs to be rebuilt).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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
