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That's what I needed, thanks! It all worked well now.
Actually using '--conform_min' preserved existing image dimensions as
desired, otherwise image got reshaped to 256^3 raising the aforementioned
dimensionality error.
Jordi
On Thu, Dec 5, 2019,
If your WM volume is not conformed, you will need to conform it with
mri_convert yourwm.mgz --conform wm.mgz
On 12/5/19 4:24 AM, Jordi Huguet wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> I have followed the suggested approach, however I get an error related
> to the
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Hi Douglas,
I have followed the suggested approach, however I get an error related to
the dimensions of the WM volume (see log trace below).
...
Found wm edits: 23448857 deletes, 783317 fills
>
> cp wm.mgz wm.seg.mgz
>
>
> mri_segment -keep
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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.
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
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
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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
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:
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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
