You can try
mris_volmask \
--label_left_white 2 --label_left_ribbon 3 \
--label_right_white 41 --label_right_ribbon 42 \
--save_ribbon $subjid
doug
On 07/08/2012 01:18 PM, Matt Glasser wrote:
> Hi Bruce,
>
> He just needs the grey matter part of a typical ribbon.mgz volume. He lost
> some of his recon-all folder.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Bruce Fischl
> Sent: Sunday, July 08, 2012 12:17 PM
> To: Colin Reveley
> Cc: [email protected]
> Subject: Re: [Freesurfer] Ribbon
>
> Hi Colin
>
> what is the representation you want in the end? You can also fill the
> interior of the surfaces using mris_fill then do some boolean algebra on
> the results of e.g. the white and pial interiors.
>
> cheers
> Bruce
>
>
> On Sun, 8 Jul 2012, Colin Reveley wrote:
>
>> Hi - I need to make a ribbon volume. I have all the necessary surfaces,
> but
>> I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the
>> list had success by just calling his orig.mgz aseg.mgz. I tried that, and
> it
>> calculated the left right pial and white distances. Men sadly it
> segfaulted.
>> The program mri_ribbon will give me separate left and white gm ribbons. I
>> combined those, coloured them 3 and 42 and did my level best to fill the
> wm
>> with the right values, but some bits are wrong.
>>
>> What I'm actually trying to do is use matt glassers myelin mapping in
> caret.
>> other things could be wrong than my ribbon estimate.
>>
>> If anyone has an idea how to make a good ribbon without aseg I'd
> appreciate
>> it. Please bear in mind I may be missing much of what one gets when one
> runs
>> recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion
>> wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the
> way
>> the bert ribbon does, so it's not that useful.
>>
>> Thanks,
>>
>> Colin
>>
>>
>
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>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[email protected]
Phone Number: 617-724-2358
Fax: 617-726-7422
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