Oh, I see now, you are including -noaseg and that is causing the problem. Why are you including that? You can rerun like
recon-all -parcstats -parcstats2 -s subject and it should regenerate the stats with the mean cortical thickness doug On 01/07/2013 02:32 PM, Deirdre O Shea wrote: > sure, here it is > > On Mon, Jan 7, 2013 at 2:24 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > hmmm, that is bizarre. Can you send me the recon-all.log file for > this subject? > > > On 01/07/2013 02:23 PM, Deirdre O Shea wrote: > > I just ran ran recon-all myself. I have attached the script i > have been using for all my subjects. > > thanks, > deirdre > > On Mon, Jan 7, 2013 at 1:45 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > I can see that the command line is not set up to create > the mean > cortical thickness, but I don't know why the arguments for the > command are not being set up properly. Did you run > mris_anatomical_stats yourself or did you just run recon-all > again? If you ran recon-all, can you send me your > recon-all script? > > doug > > > > On 01/07/2013 01:25 PM, Deirdre O Shea wrote: > > Thanks Doug, > > I have attached two files. You will see in > 'aparc.stats' that > there is no mean for cortical thickness and in the > aparc.stats2 file there is. > > thanks > Deirdre > > On Mon, Jan 7, 2013 at 12:48 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > Can you send the aparc.stats file in question? > doug > On 01/07/2013 11:44 AM, Deirdre O Shea wrote: > > Dear FreeSurfers, > > > > My query relates to the aparc stats file in > FreeSurfer. > Upon the > > editing and reconstruction of my subjects I have > noticed > that > the Mean > > Thickness for the cortex was missing, i.e., no > value was > provided > > despite it being there before I ran another > reconstruction. > While this > > has only occurred in a couple of my subjects (out of > many) I'm > > wondering what may be the cause and how I may I > now go > about getting > > this value? > > > > > > Best, > > Deirdre > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
