Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Douglas N Greve]

You can use
mri_convert aseg.mgz --erode-seg 1 aseg.e1.mgz
and visualze aseg.e1.mgz vs aesg.mgz
you can use aseg.e1.mgz as input to mri_segstats (and turn off the erode)

On 04/15/2016 11:08 AM, Elijah Mak wrote:
>
> Hi Doug,
>
> I have pasted the previous emails below. I have computed mri_segstats 
> to extract the FA and MD from resampled aparc+aseg.mgz in diffusion 
> space. -seg-erode 1 was performed during mri_segstats. Now, I will 
> like to visually inspect the results of that erosion for the left and 
> right hippocampal structures. Is there anyway I can do that and 
> compare that against the uneroded hippocampus?
>
>  I don't think mri_segstats -seg-erode 1 produce any volumetric 
> outputs so I am not sure.
>
> Thanks.
>
> Best Wishes,
>
> Elijah
>
>
> Douglas N Greve 
> 
>  
> Mon, 11 Apr 2016 08:11:06 -0700 
> 
>
> You can load it as an overlay in freeview make sure to specify the 
> registration file as that compted for the DTI. Also make sure to set 
> the threshold to something like 0.5
> On 04/11/2016 09:41 AM, Elijah Mak wrote: > Hi Freesurfer Community, > 
> > I have performed -seg-erode 1 during mri_segstats on resampled > 
> subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 
> > anatomical space to visually inspect whether PVE has been adequately 
> > accounted for? > > Thank you. > > Best Wishes, > Elijah
>
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Douglas N Greve]

Hi Elijah, please remember to include previous correspondences in each 
email. I don't remember what this was about.
doug

On 04/11/2016 11:37 AM, Elijah Mak wrote:
> Thanks Doug.
>
> Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on 
> the orig.mgz as an overlay? I am able to do that but I can't seem to 
> find an option for thresholding. Sorry if I misunderstood your 
> original email.
>
> Best Wishes,
> Elijah
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Thanks Doug.

Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the
orig.mgz as an overlay? I am able to do that but I can't seem to find an
option for thresholding. Sorry if I misunderstood your original email.

Best Wishes,
Elijah
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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Douglas N Greve]

You can load it as an overlay in freeview make sure to specify the 
registration file as that compted for the DTI. Also make sure to set the 
threshold to something like 0.5

On 04/11/2016 09:41 AM, Elijah Mak wrote:
> Hi Freesurfer Community,
>
> I have performed -seg-erode 1 during mri_segstats on resampled 
> subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 
> anatomical space to visually inspect whether PVE has been adequately 
> accounted for?
>
> Thank you.
>
> Best Wishes,
> Elijah
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Hi Freesurfer Community,

I have performed -seg-erode 1 during mri_segstats on resampled subcortical
strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space
to visually inspect whether PVE has been adequately accounted for?

Thank you.

Best Wishes,
Elijah
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