Re: [Freesurfer] pial surface crossing white

[Harms, Michael]

Yeah, the time stamps look fine, and the euler numbers are correct. I've uploaded the pre-edited (L408_base_orig.tgz) and edited (L408_base.tgz) directories. This was related to the creation of a 'base' template, so the commands are a little bit involved.  For the "L408_base_orig" set of data: recon-all -base L408_base -tp L408_110502 -tp L408_120817 -tp L408_130819 -all -mprage -expert expert.opts For the edits in "L408_base": recon-all -base L408_base -tp L408_110502 -tp L408_120817 -tp L408_130819 -autorecon2-wm -autorecon3 -mprage Hopefully you can investigate without needing the "cross" time points, but if you need those, I could ftp those as well. thanks, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu On 9/29/14 8:49 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: Hi Mike that's really strange. Are you sure you recreated the pial??? Can you double check time-stamps and such? And Euler number to make sure that it is the same for white and pial? If that all looks right, upload the subject and send me the command line you used for the rerunning and I'll investigate. cheers Bruce On Wed, 24 Sep 2014, Harms, Michael wrote: Hi, We are seeing some instances where the pial surface is crossing over the white surface in the vicinity of the precuneus and lingual cortex, where there is only a thin strand of WM separating the GM from the lateral ventricle.  In these cases, it appears that GM is getting labeled as "WM-hypointensities" in the aseg, and then assigned a value of 250 in the wm.mgz.  So, we deleted those erroneous values in the wm.mgz (changing them from 250 to 1).  The resulting white surfaces following these edits are a much better reflection of where the white surface should be, but the pial surface still crosses over into the WM.  See attached png's for examples in two subject, where there are both "PreWMedit" and "PostWMedit" snapshots for each of the two subjects.  (In each of the attached examples, the issue is on the left hemi -- i.e,. right side of the snapshot). My question is:  Is there some other way that we are supposed to edit this?  Or, having fixed the gross errors in the white surface, do we just have to accept the remaining inaccuracy in the pial surface.  It's a fairly localized remaining error in the pial surface, but I'm puzzled how it ends up on the wrong side of the white surface to begin with. thanks, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu   ________________________________________________________________________________________________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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