Hi AJ,

Did you already use the --lesion-mask-pattern flag for the T2 contrast (Cf. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/Samseg)? The default behavior will mask lesion voxels with respect to the cortical gray matter, but you can also try to relax the constraint by masking them with respect to the white matter (you need to include the flag --lesion-mask-structure 'White'). 

Also, instead of trying different --threshold flags, you can save segmentation maps with the flag --save-posteriors and check the lesions map at /yourOutput/posteriors/Lesion.mgz. This volume will give you a rough idea of which threshold is the most suitable.

If lesions are still not segmented well, as last resort you can always manually edit them from the seg.mgz.

Hope it helps.

Best,
Stefano

---

From: AJ <ajcns1969@gmail.com>
Sent: 26 April 2021 04:52
To: Freesurfer support list
Cc: Stefano Cerri
Subject: Re: [Freesurfer] T2 lesion editing

 

Many thanks.

Best.

AJ

On Sun, Apr 25, 2021, 21:45 Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 4/24/2021 5:56 PM, AJ wrote:

        External Email - Use Caution        

Hi,

Once SAMSEG has finished segmenting T2 lesions, other than trying different --threshold flags, any way to manually modify them?

I'll let Stefano (cc'ed) weigh in.

Can --eTIV be added to SAMSEG?

Not sure what you mean here. There is an etiv value that is output in the samseg folder

In Samseg, can brainstem be segmented into parts, such as medulla, pons, mid brain like through recon all?

No, not yet

Can corpus callosum be segmented separately in Samseg?

I have not tried this, but you can try
mri_cc -aseg seg.mgz -o seg.cc.mgz

Sorry for all the questions.

Many thanks.

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