Hi Elijah

no, we don't have the resources to document, test, distribute and support it. I wish we did

sorry Bruce

On Wed, 18 May 2016, Elijah Mak wrote:

                             Hi Martin,

I am also following this thread with interest. Is that multi-modal prototype you mentioned available in the next FS6.0?

                            Many thanks.




                            Best Wishes,

                               Elijah




       Navena Rebecca Lingum Wed, 18 May 2016 10:25:09 -0700

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

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From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Martin Reuter mreu...@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 thin k 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 modaliti es.

Best, Martin

P.S. Changed the subject, to reflect that this is not a longitudinal questio n 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" o f 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 pro per segmentation of WMH would require a T2w Flair (which I have). How do I go ab out combining the preprocessing data produced by FreeSurfer with my T2w images t o 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 <mreu...@nmr.mgh.harvard.edumailto:mreu...@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 t he 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 usin g the recon-all command?

Navena Lingum

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-- 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

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Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ