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 
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?


On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl 
<<>> 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


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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