I'm not actually sure. What are the files that appeared there? On Tue, 1 Feb 2011, Cheryl McCreary wrote:
> 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. >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
