Dear experts, I noticed that my original mail did not appear in mail archive, therefore I am reposting, to prevent this request left unattended. The reason of omitting the original post from mail archive was probably the attachments (screenshots). Therefore this time I am reposting without attachments. They are included in the original mail.
Best regards and merry Christmas, Antonin Skoch From: Antonin Skoch <a...@ikem.cz> To: <freesurfer@nmr.mgh.harvard.edu> Sent: 12/21/2016 1:41 AM Subject: pial surface errors - V6beta Dear experts, in my data I quite often encounter errors in pial surface which is probably induced by errors of white surface, in some cases caused by juxtacortical lesions (even in healthy subjects). See screenshots for examples. I have tested this on freesurfer V6 beta but it is commonly also found in older versions. I have uploaded the subject pial_errors.tar.gz to your server. The error showed pial_error1.png in probably caused by small error in white surface shape in 18,-18,63 (RAS). Another similar problem is in 15,10,53 (RAS). This is probably caused by juxtacortical lesion. Another problematic spot with juxtacortical lesion is on -7,18,47 (RAS). I have observed such kind of errors in quite a large number of subjects, these are either healthy controls or subjects with psychiatric ilnesses, therefore no particular apparent macroscopic pathology should be present in these subjects. Do you think that there could be some improvement in the mris_make_surfaces code to prevent this kind of behaviour (i.e. very small error in white has gross effect on pial), or it is necessary in all these cases to manually intervene ? Especially, I do not see any particular problem in image in case of pial_error1.png. And, in case of editing of problems errors by juxtacortical lesions I find fastest way to edit wm (due to the fact that I can constrain the brush not to draw to existing wm) in contrast to editing aseg (i.e. label the spot as a lesion). Do you think that aseg editing in contrast to wm editing has some benefit in this case? Regards, Antonin Skoch
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