Hi Bruce,
In both versions, I use this command:
mris_flatten rh.occip.patch.3d rh.occip.patch.flat
They are applied to the same patch.
Also may be I missed it but when I used help (mris_flatten --help) I didn't see
any of these flags.
Regards,
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution
Hi Shahin
What is your command line? mris_flatten does some random sampling of distances
since the whole N^2 distance matrix is too big. You can remove the randomness
by either specifying -norand or using a specific seed like -seed 1234.
That said, you second image looks like a failure of the flattening. This
usually means the distances aren’t sampled out far enough/densely enough. The
defaults are super old (7 neighbor ring, 12 distances/ring). You could try
something like -distances 20 20 and see if that fixes things (and -norand if
you want)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 3:15 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution
Hi Surfers,
This is the second time that I have brought this issue up. When applied
to the same 3D patch, the command mris_flatten generates two completely
different outcomes when runs under stable 6 vs. 711 (see the attached files). I
checked the documentation if there is any flags by which I can control the
process. But I couldn't find anything relevant. Any idea what has happened?
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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