Fwd: Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter".
---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom linnnorbom@gmail.com Date: Mon, Feb 3, 2014 at 5:44 PM Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter". To: Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi again,
Sorry for being unclear. Here is a picture of the lesion. If I understand correctly it is now NOT included as white matter. All I want to do is include it as white matter, so that it will be registered as a hypo-intense area in aseg.stats.
So the way to do this is to edit the aseg.mgz and not the wm.mgz?
Cheers Linn Norbom
On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Linn I'm not sure I understand, but if you can paste them into the aseg.mgz as hypointensities I think things should work properly
cheers Bruce
On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote:
Hi,
I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the statistic volume of these areas as hypo-intense-wm in the aseg.stats?
Thank you in advance, Regards Linn Norbom
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Hi Linn
it looks like a hypo intense region surrounded by a hyper-intense one, no? I think if you edit those voxels in the aseg.mgz to be "white matter hypointensities" or "lesion" then run the recon from there forward it should be ok Bruce
On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote:
---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom linnnorbom@gmail.com Date: Mon, Feb 3, 2014 at 5:44 PM Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter". To: Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi again, Sorry for being unclear. Here is a picture of the lesion. If I understand correctly it is now NOT included as white matter. All I want to do is include it as white matter, so that it will be registered as a hypo-intense area in aseg.stats. So the way to do this is to edit the aseg.mgz and not the wm.mgz? Cheers Linn Norbom
On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Linn I'm not sure I understand, but if you can paste them into the aseg.mgz as hypointensities I think things should work properly
cheers Bruce On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote: Hi, I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the statistic volume of these areas as hypo-intense-wm in the aseg.stats? Thank you in advance, Regards Linn NorbomThe 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.
use mri_binarize --replace 77 2 --i aseg.mgz --o aseg.linn.mgz
use the mri_binarize from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
then use something like this to generate the new stats table (you'll have to customize it)
mri_segstats --seg mri/aseg.linn.mgz --sum stats/aseg.linn.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject yousubjectname
On 02/03/2014 12:11 PM, Linn Christin Bonaventure Norbom wrote:
---------- Forwarded message ---------- From: *Linn Christin Bonaventure Norbom* <linnnorbom@gmail.com mailto:linnnorbom@gmail.com> Date: Mon, Feb 3, 2014 at 5:44 PM Subject: Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into "normal white matter". To: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
Hi again, Sorry for being unclear. Here is a picture of the lesion. If I understand correctly it is now NOT included as white matter. All I want to do is include it as white matter, so that it will be registered as a hypo-intense area in aseg.stats. So the way to do this is to edit the aseg.mgz and not the wm.mgz? Cheers Linn Norbom
On Mon, Feb 3, 2014 at 5:30 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Linn I'm not sure I understand, but if you can paste them into the aseg.mgz as hypointensities I think things should work properly cheers Bruce On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote: Hi, I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the statistic volume of these areas as hypo-intense-wm in the aseg.stats? Thank you in advance, Regards Linn Norbom 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.
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