For instructions I used the link FS Tutorial/SkullStripFix on http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction
The files that appeared in the subject mri directory were COR-info and COR-001, COR-002 ... COR-256. I assumed that these refer to the number of segments in the 3D MRI volume that was acquired in the coronal direction. On 2/1/11 2:02 PM, "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote: > and what wiki page were you following? (some of our wiki pages are no > longer used but still exist on the site) > > > On Tue, 2011-02-01 at 15:59 -0500, Allison Stevens wrote: >> 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 >> >> > > -- 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
