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-request@nmr.mgh.harvard.edu wrote:
Message: 5 Date: Wed, 10 Jan 2018 20:26:11 +0000 From: "Rockers, Elijah D." <edrockers@houstonmethodist.orgmailto:edrockers@houstonmethodist.org> Subject: [Freesurfer] reconstruction for very significant atrophy To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <1515615971.3868.3.camel@houstonmethodist.orgmailto:1515615971.3868.3.camel@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 white/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 aggressively 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHos... and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMeth.... ***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. -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu...
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Message: 6 Date: Wed, 10 Jan 2018 15:28:25 -0500 (EST) From: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] reconstruction for very significant atrophy To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1801101527330.32719@gate.nmr.mgh.harvard.edumailto:alpine.LRH.2.20.1801101527330.32719@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Eli
it's hard to say without looking at an image. Can you upload a subject and point us at a spot you think is incorrect? And do you really think the thickness should be 0 - there is no gray matter left at all? That seems unlikely....
cheers Bruce
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-request@nmr.mgh.harvard.edu wrote:
Message: 5 Date: Wed, 10 Jan 2018 20:26:11 +0000 From: "Rockers, Elijah D." edrockers@houstonmethodist.org Subject: [Freesurfer] reconstruction for very significant atrophy To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 1515615971.3868.3.camel@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 an d is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHos... &c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=CAYGC 0ZOLxrUbIrT78SfflAkZfYgzH8oPSEwBFUSUJg&s=PGX_syFrdnwd33_SeD4mJhR7objuPhwbK4lqK8C1R-M&e= and https:// urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMethodist&d=DwICAg&c=QmPtDiFixEjkMvD KaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=CAYGC0ZOLxrUbIrT78SfflA kZfYgzH8oPSEwBFUSUJg&s=04vdwvZSyWy5SG-GmsAzYUrtI0lyfQC__axac_6TQzM&e=. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain res tricted and privileged material for the sole use of the intended recipient(s). Any review, use, dist ribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or a uthorized to receive for the recipient), please contact the sender and delete all copies of the mess age. Thank you.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rockers, Elijah D.