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.edumailto: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 CautionHi 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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