The entire result overlay appears shifted, yes. Put differently, we are seeing significant results in the regions just a bit superior to the regions we know to have atrophy. I am just wondering if there is something else I can check in the pipeline to make sure everything is lining up correctly before the glmfit analysis. Like just in case some of the subjects are not accurately registered into the common space used for the vertex-wise analysis.
FYI we are comparing 8 diseased (nonfluent PPA) subjects to ~40 controls. I have manually checked the segmentations for all these images, and they are accurate. Thanks for your help, -Eli On Thu, 2018-01-11 at 11:43 -0500, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 3 Date: Thu, 11 Jan 2018 11:02:41 -0500 (EST) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] reconstruction for very significant atrophy To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.lrh.2.20.1801111102310.32...@gate.nmr.mgh.harvard.edu<mailto:alpine.lrh.2.20.1801111102310.32...@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" do you mean that the entire surface is off by a fixed amount? On Thu, 11 Jan 2018, Rockers, Elijah D. wrote: Thanks Bruce. I went over some more images with our PI and he was mostly satisfied with the pial/white segmentations. The real problem here is that our results look correct, except for they seem to be translated vertically by a small amount, comparing with what we see on the MRIs. What can we check to make sure everything is lining up correctly? - Eli On Thu, 2018-01-11 at 08:08 -0500, freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: Message: 5 Date: Wed, 10 Jan 2018 20:26:11 +0000 From: "Rockers, Elijah D." <edrock...@houstonmethodist.org<mailto:edrock...@houstonmethodist.org>> Subject: [Freesurfer] reconstruction for very significant atrophy To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <1515615971.3868.3.ca...@houstonmethodist.org<mailto:1515615971.3868.3.ca...@houstonmethodist.org>> Content-Type: text/plain; charset="utf-8" Hello, We have some images that reflect severe atrophy in some subjects, in which gray matter is virtually undetectable on the MRI in some regions. However, upon checking the segmentations visually, the whit e/pial surfaces are reflecting a significant cortical thickness in these areas. Is there perhaps any recon-all setting that might extend the white matter area out a little more agg ressively than it does with the default settings? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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