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Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.n...@mgh.harvard.edu>
Sent: Saturday, April 8, 2023 8:59 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Fischl, Bruce R.,PHD <bfis...@mgh.harvard.edu>
Subject: Re: mris_flatten Version 6 vs. 7
Dear Bruce,
I ran mris_flatten with -norand flag (mris_flatten -norand
rh.occip.patch.3d rh.occip.patch.flat) and it still fails (see the attached
file). I can share the patch with you if you want. But it is a surprise
because version 6 generate the flattened patch without any problem.
Also FYI, this problem is NOT limited to this specific patch. I have
applied it to multiple other occipital patches (from other subjects) and the
outcome is the same.
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, April 7, 2023 5:21 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
Yes, well, that is totally my fault! Doug is much better about adding help text
than I am ☹
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 5:18 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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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