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Great, just what I was looking for!

Thanks Douglas,
Jordi

On Wed, Nov 27, 2019, 19:47 Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
wrote:

> It might work if you
> mkdir -p FOO/mri
> cp yourwm.mgz FOO/mri/wm.mgz
> cp inputdata.mgz FOO/mri/orig/001.mgz
> then run recon-all -s FOO -all
>
>
> On 11/27/2019 12:39 PM, Jordi Huguet wrote:
>
>         External Email - Use Caution
> Hi Bruce,
>
> Many thanks for your reply.
>
> I understand from your answer that it could be done as follows (I am not
> an expert in FreeSurfer directives):
>
> a) run full FreeSurfer pipeline
> recon-all -s FOO
> b) insert pre-existing WM segmentation as wm.mgz (modifying the intensity
> values)
> c) re-run stages 15-23 and 24-31 (recon-all shall use my external
> segmentation as WM "edits")
> recon-all -s FOO -autorecon2-wm -autorecon3
>
> Is it possible however to just include the WM segmentation without
> executing a full early run of recon-all?
>
> Thanks,
> Jordi
>
>
> On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Jordi
>>
>> yes, this should be possible. You might need to run recon-all in stages
>> though. Although if you set the wm.mgz values from SPM to 255 and 1 (not
>> 0)
>> recon-all should detect them as "edits" and retain them
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 26 Nov 2019, Jordi Huguet wrote:
>>
>> >
>> >         External Email - Use Caution
>> >
>> > Hi there,
>> > I wonder if its somehow possible to feed FreeSurfer's recon-all with
>> pre-existing segmented maps
>> > (based on prior segmentation procedure e.g. SPM or ANTs) to
>> "improve" FreeSurfer results.
>> >
>> > For some images I am working with the FreeSurfer's WM segmentation
>> output is not optimal so I am
>> > looking for alternatives to improve the final results on such specific
>> cases without requiring any
>> > manual intervention.
>> >
>> > Any comments, examples or shared reflections on this regard are kindly
>> welcome.
>> >
>> > Thanks in advance,
>> > Jordi Huguet
>> >
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>
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