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Can you try running it with -distances 20 20 added to the command line?

 

From: Nasr, Shahin,Ph.D. <shahin.nasr@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 <BFISCHL@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,

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu>
Sent: Friday, April 7, 2023 5:21 PM
To: Freesurfer support list <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@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

 

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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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