Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
Hi Navena,
There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates.
Best, Martin
On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote:
Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Martin,
Thank you kindly for your prompt response.
I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere.
As it stands, I am finding it difficult to understand the exact “pipeline” of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats?
Any help on the matter is much appreciated!
Kindly, Navena Lingum
On May 16, 2016, at 4:24 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Navena,
There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates.
Best, Martin
On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
Hi Navena,
I am the wrong person to answer questions about the WM lesion stream. I think the one that is available in FreeSurfer is only based on T1 images, but a prototype of a better stream exists, that can incorporate different modalities.
Best, Martin
P.S. Changed the subject, to reflect that this is not a longitudinal question any more.
On 05/17/2016 12:37 PM, Navena Rebecca Lingum wrote:
Dear Martin,
Thank you kindly for your prompt response.
I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere.
As it stands, I am finding it difficult to understand the exact “pipeline” of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats?
Any help on the matter is much appreciated!
Kindly, Navena Lingum
On May 16, 2016, at 4:24 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Navena,
There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates.
Best, Martin
On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote:
Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Would any member of the FreeSurfer team be able to help with this question?
I would like to use the FreeSurfer software to delineate white matter hyperintensities. I have processed my T1 images using the recon-all command, and in the aseg.stat file there is a value for WM hypointensities.
Is there an alternate stream/ FreeSurfer algorithm that exists for the processing of T2w FLAIR images for WM hyperintensities?
Thanks, Navena
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: May 17, 2016 1:32 PM To: Freesurfer support list Subject: [Freesurfer] WM Hyperintensities
Hi Navena,
I am the wrong person to answer questions about the WM lesion stream. I think the one that is available in FreeSurfer is only based on T1 images, but a prototype of a better stream exists, that can incorporate different modalities.
Best, Martin
P.S. Changed the subject, to reflect that this is not a longitudinal question any more.
On 05/17/2016 12:37 PM, Navena Rebecca Lingum wrote: Dear Martin,
Thank you kindly for your prompt response.
I am actually having difficulties with the delineation of White Matter Hyperintensities at a single time point. I apologize if my question is redundant and perhaps an answer to it is already mentioned elsewhere.
As it stands, I am finding it difficult to understand the exact "pipeline" of commands necessary to perform this segmentation and accurate delineation of WMH. I have ran the recon -all command on my T1w images, but I suspect a proper segmentation of WMH would require a T2w Flair (which I have). How do I go about combining the preprocessing data produced by FreeSurfer with my T2w images to produce a WMH mask/volume/stats?
Any help on the matter is much appreciated!
Kindly, Navena Lingum
On May 16, 2016, at 4:24 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Navena,
There is currently no dedicated stream for longitudinal WM abnormalities (in the sense of joint estimation and modeling). You can, however, make use of the longitudinal stream and it's increase reliability - e.g it is working in the same space across time, which should help get more reliable estimates.
Best, Martin
On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote: Dear FreeSurfer experts,
My colleagues and I would like to use FreeSurfer to perform a longitudinal analysis of white matter hyperintensities. Is there an additional add-on for the software to perform this analysis or can this analysis be performed using the recon-all command?
Navena Lingum
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu
freesurfer@nmr.mgh.harvard.edu
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Martin Reuter -
Navena Rebecca Lingum