Hi Allison, Is there a way into incorporate these files into the brainmask without having to redo the edits? I processed a number of subjects this way, using 'save main volume as' as directed in the recommended recon workflow.
Thanks, Cheryl On 1/31/11 7:05 PM, "Allison Stevens" <astev...@nmr.mgh.harvard.edu> wrote: > Hi Cheryl, > 1) Yes, just use save not save as > 2) this information is already generated and can be found in the > aseg.stats in each subject's stats dir. Some of the information is at the > top of that file. > > On Mon, 31 Jan 2011, Cheryl McCreary wrote: > >> Hi, >> >> I'm new to Freesurfer and am trying to process some data for the first >> time. I have two questions: >> >> 1. I have done some manual editing of the brainmask for skullstripping, >> saving the edits using 'Save As' and the default names. This seems to create >> a new group of files separate from the brianmask, in the mri subdirectory. >> Are these edits incorporated in the brainmask when autorecon2 and autorecon3 >> are run? I ask because the pial surfaces viewed using tkmedit after >> processing is complete often extends into the dura and unstripped skull that >> remains visible on the brainmask, even though it was removed in manual >> editing. Should I be using 'Save' instead of 'Save as' after editing? >> >> 2. For then initial analysis of my data, I would like to create a table of >> intracranial volume, brain parenchymal volume, gray matter volume and white >> matter volume. I've tries using the following command line: >> >> mri_segstats --sum TableFileName.sum >> --pv $SUBJECTS_DIR/Subject/mri/norm.mgz >> --ctab-default >> --surf-ctxgmwm >> --etiv $SUBJECTS_DIR/Subject/mri/transforms/talairach.xfm >> >> However, this fails with the error: unknown option --surf-ctxgmwm. >> >> What have I missed? Can you recommend another way to get this information? >> I have also tried asegstats2table as well, but intracranial volume was not >> included in the table. >> >> Thank you for any assistance or suggestions. >> >> Kind regards, >> Cheryl >> >> >> >> >> _______________________________________________ >> 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. > > -- Cheryl McCreary, PhD Research Scientist Seaman Family MR Research Centre Foothills Medical Centre 1403 29th Street NW Calgary, AB T2N 2T9 Phone: (403) 944-8781 FAX: (403) 270-7907 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
