From: Christine Smith <cnsm...@ucsd.edu> Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser <m...@ma-tea.com> Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan
Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom picture. Please find attached a dicom picture that is oriented the same way as freesurfer. Sorry for any confusion. On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith <cnsm...@ucsd.edu> wrote: > Dear Matt, > > Please find attached two pictures. One is of the brain from reconstructed > dicom files (using AFNI). The other one is a pic from tkmedit of the same > subject and approximately the same slice of brain. Notice that the freesurfer > image is very bright. Look at the white matter and pial lines (i.e., cortical > thickness) in the upper left hand part of the image and see how thin the > cortex appears. Notice also, that there is very little grey/white contrast in > this same area in the brain image reconstructed from dicoms. > > Please let me know if there are any other pictures you might desire or > information you might need. > > Christine > > > On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser <m...@ma-tea.com> wrote: >> Some pictures would probably be helpful to know what the issue is. >> >> Peace, >> >> Matt. >> >> From: Christine Smith <cnsm...@ucsd.edu> >> Date: Thursday, January 23, 2014 1:05 PM >> To: <freesurfer@nmr.mgh.harvard.edu> >> Subject: [Freesurfer] poor grey/white distinction in superior part of scan >> >> Hello, >> >> I am emailing to inquire about whether poor grey/white contrast in one part >> of a scan (i.e., the posterior and superior part of the scan; ~parietal >> cortex) can be addressed. The contrast in other parts of the scan looks good >> and freesurfer does a great job of distinguishing white from grey. For the >> parietal cortex area the cortex appears very thin. In addition, the entire >> brain appears 'white' or bright, even though the brain doesn't look this >> bright if you reconstruct it from dicoms. >> >> We have now obtained 4 scans like this, so it isn't just one person with >> thinning cortex. >> >> How can I make an adjustment to only this superior part of the brain and >> leave the rest of it alone? Or do I need to make an adjustment to the >> intensity early on for the entire scan and then basically start over with >> editing? >> >> Best, >> Christine >> >> -- >> Christine N. Smith, Ph.D. >> Department of Psychiatry >> University of California, San Diego >> _______________________________________________ Freesurfer mailing list >> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin >> fo/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. > > > > -- > Christine N. Smith, Ph.D. > Department of Psychiatry > University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego
<<attachment: dicom_flipped.jpg>>
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