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:

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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 <fischl@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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