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 [fischl@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

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From: Bruce Fischl [fischl@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

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From: Bruce Fischl [fischl@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

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