Hi Bruce, Doug, and All, I have corrected a boundary between lh corpuscallosum and caudalanteriorcingulate.
I have overwritten the label/lh.aparc.annot as per Bruce's email below. However, doesn't this leave a number of files with incorrect information now in the stats directory? Do I need to rerun something to bring these up to date? Thanks, Helen ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, July 11, 2011 2:57 PM To: Keefe, Helen L Subject: RE: [Freesurfer] save label after expand boundary of region sure. Good luck Bruce On Mon, 11 Jul 2011, Keefe, Helen L wrote: > Thank you! > > This will help me clear up a lot of problem scans - I really appreciate your > help > > Helen > > > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Monday, July 11, 2011 2:42 PM > To: Keefe, Helen L > Subject: RE: [Freesurfer] save label after expand boundary of region > > no, it won't matter > On Mon, 11 Jul 2011, Keefe, Helen L wrote: > >> Hi Bruce - >> >> I made the edits on the pial surface using command: >> >> >> tksurfer $i lh pial -annotation aparc >> >> >> Does that make any difference? Since the instructions say to use the >> inflated surface: >> >> tksurfer -annot aparc subjectid rh inflated >> >> Thanks, >> Helen >> >> ________________________________________ >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Monday, July 11, 2011 11:31 AM >> To: Keefe, Helen L >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] save label after expand boundary of region >> >> if you export it as an annotation then all the labels will be combined in >> one file. I think you are probably editing the ?h.aparc.annot, so you could >> overwrite that one if you want. The correct mri_segstats command could then >> be found in the subject's recon-all.log or recon-all.cmd file in the >> scripts dir. >> >> cheers >> Bruce >> >> >> On Mon, 11 Jul 2011, Keefe, Helen L wrote: >> >>> Hi Bruce, Doug, and All: >>> >>> Questions on a continuing problem: >>> >>> When I run tksurfer, the caudalanteriorcingulate is invaded by the >>> corpuscallosum. >>> I edited the boundary using the instructions at: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit >>> >>> I'm then instructed to "Save the annotation: File > Label > Export >>> Annotation. Probably choose a new name rather than writing over an existing >>> file" >>> >>> I don't need a new name - I just need to save the labels for the >>> caudalanteriorcingulate and the corpuscallosum, which both now look >>> correct. How/where >>> do I do that? Here are the files in the label dir: >>> >>> lh.cortex.label >>> lh.aparc.annot >>> lh.aparc.a2009s.annot >>> rh.cortex.label >>> rh.aparc.annot >>> aparc.annot.ctab >>> rh.aparc.a2009s.annot >>> aparc.annot.a2009s.ctab >>> >>> >>> Also - >>> >>> I previously asked what I need to do after that to ensure accurate >>> measurements. >>> Bruce responded, >>> "I don't think you need recon2 since you are just changing the aparc. I >>> believe you can just run the aparc stats step, but I'll cc Doug who might >>> know >>> better." >>> >>> Any advice on all this? >>> >>> Thanks, >>> Helen >>> >>> >>> __________________________________________________________________________________________________________________________________________________________ >>> Notice: This UI Health Care e-mail (including attachments) is covered by >>> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >>> confidential >>> and may be legally privileged. 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