External Email - Use Caution
Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached).
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FS... ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Subject: RE: mris_flatten Version 6 vs. 7
Oh, looks like you had a small cut there
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
In the attached file, I zoomed in and enlarged the location so you can see the issue.
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FS...
________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor)
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that?
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FS...
________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto: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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FS...
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FS...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
External Email - Use Caution
I think it’s just a slight overlap of the flat map. In the FS6 version, using the sulcal pattern as a reference you can see that the calcarine cut does go all the way to that point/vertex. If you were to select two vertices on either side of the “bridge” and make a path, the path would curve around instead of cutting straight across.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Date: Saturday, April 8, 2023 at 4:34 PM To: Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU, freesurfer (freesurfer@nmr.mgh.harvard.edu) freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached).
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HD-HNxf0EDKilS-qMTfzklTm7L5obuRkCIgmbsdLmD-PhG...https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FSXa1UpRyhBZRvfuv7kInq7uQgMPJoxIShEFBbTMJ8gyAnNCX3d5hnKF8iBa_PkBTVhkDmbIyQoEOWuvS1AWQezeNbZRerJ8eFVUlFIis6M92nKiPLjUKUvf5Dtb1RjL6Aheqs35hmzHSP9UJzSr0kcbGcOjLlE2m0S3n1zeLmfumwWoSI7pAAEYfbKbjhf5pCNushUeAX6JUwQiTSpH0WMwZZ5qpB07YYBUKunkMg/https%3A%2F%2Fmesovision.martinos.org%2F ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Subject: RE: mris_flatten Version 6 vs. 7
Oh, looks like you had a small cut there
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
In the attached file, I zoomed in and enlarged the location so you can see the issue.
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HD-HNxf0EDKilS-qMTfzklTm7L5obuRkCIgmbsdLmD-PhG...https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FSXa1UpRyhBZRvfuv7kInq7uQgMPJoxIShEFBbTMJ8gyAnNCX3d5hnKF8iBa_PkBTVhkDmbIyQoEOWuvS1AWQezeNbZRerJ8eFVUlFIis6M92nKiPLjUKUvf5Dtb1RjL6Aheqs35hmzHSP9UJzSr0kcbGcOjLlE2m0S3n1zeLmfumwWoSI7pAAEYfbKbjhf5pCNushUeAX6JUwQiTSpH0WMwZZ5qpB07YYBUKunkMg/https%3A%2F%2Fmesovision.martinos.org%2F
________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor)
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that?
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HD-HNxf0EDKilS-qMTfzklTm7L5obuRkCIgmbsdLmD-PhG...https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FSXa1UpRyhBZRvfuv7kInq7uQgMPJoxIShEFBbTMJ8gyAnNCX3d5hnKF8iBa_PkBTVhkDmbIyQoEOWuvS1AWQezeNbZRerJ8eFVUlFIis6M92nKiPLjUKUvf5Dtb1RjL6Aheqs35hmzHSP9UJzSr0kcbGcOjLlE2m0S3n1zeLmfumwWoSI7pAAEYfbKbjhf5pCNushUeAX6JUwQiTSpH0WMwZZ5qpB07YYBUKunkMg/https%3A%2F%2Fmesovision.martinos.org%2F
________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto: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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HD-HNxf0EDKilS-qMTfzklTm7L5obuRkCIgmbsdLmD-PhG...https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FSXa1UpRyhBZRvfuv7kInq7uQgMPJoxIShEFBbTMJ8gyAnNCX3d5hnKF8iBa_PkBTVhkDmbIyQoEOWuvS1AWQezeNbZRerJ8eFVUlFIis6M92nKiPLjUKUvf5Dtb1RjL6Aheqs35hmzHSP9UJzSr0kcbGcOjLlE2m0S3n1zeLmfumwWoSI7pAAEYfbKbjhf5pCNushUeAX6JUwQiTSpH0WMwZZ5qpB07YYBUKunkMg/https%3A%2F%2Fmesovision.martinos.org%2F
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HD-HNxf0EDKilS-qMTfzklTm7L5obuRkCIgmbsdLmD-PhG...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
External Email - Use Caution
Thanks Louis! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Vinke, Louis N.,PHD Sent: Tuesday, April 11, 2023 6:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution I think it’s just a slight overlap of the flat map. In the FS6 version, using the sulcal pattern as a reference you can see that the calcarine cut does go all the way to that point/vertex. If you were to select two vertices on either side of the “bridge” and make a path, the path would curve around instead of cutting straight across.
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: Saturday, April 8, 2023 at 4:34 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>, freesurfer (freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu) <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached).
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ecznVBbK3IxzRI10oacqvODfgiESwO8Ywx2bhcr5T_YsG3...https://secure-web.cisco.com/11YPf2MPvXvH0nit4jHDe36YSTq-NvOFFUASunejUkkR9FSXa1UpRyhBZRvfuv7kInq7uQgMPJoxIShEFBbTMJ8gyAnNCX3d5hnKF8iBa_PkBTVhkDmbIyQoEOWuvS1AWQezeNbZRerJ8eFVUlFIis6M92nKiPLjUKUvf5Dtb1RjL6Aheqs35hmzHSP9UJzSr0kcbGcOjLlE2m0S3n1zeLmfumwWoSI7pAAEYfbKbjhf5pCNushUeAX6JUwQiTSpH0WMwZZ5qpB07YYBUKunkMg/https%3A%2F%2Fmesovision.martinos.org%2F ________________________________ From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Subject: RE: mris_flatten Version 6 vs. 7
Oh, looks like you had a small cut there
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
In the attached file, I zoomed in and enlarged the location so you can see the issue.
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor)
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that?
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto: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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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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External Email - Use Caution
Correct Luis. But I am not sure why did verion 7 act like this.
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/1dieRkuIGIwcoRKWXF1_E_U5H9RTe-srddJwMy53L6NZ99m... ________________________________ From: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Tuesday, April 11, 2023 6:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Subject: RE: mris_flatten Version 6 vs. 7
Thanks Louis! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Vinke, Louis N.,PHD Sent: Tuesday, April 11, 2023 6:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
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I think it’s just a slight overlap of the flat map. In the FS6 version, using the sulcal pattern as a reference you can see that the calcarine cut does go all the way to that point/vertex. If you were to select two vertices on either side of the “bridge” and make a path, the path would curve around instead of cutting straight across.
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: Saturday, April 8, 2023 at 4:34 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>, freesurfer (freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu) <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution
Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached).
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Subject: RE: mris_flatten Version 6 vs. 7
Oh, looks like you had a small cut there
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
In the attached file, I zoomed in and enlarged the location so you can see the issue.
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor)
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that?
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto: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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mris_flatten Version 6 vs. 7
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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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In occipital flat map cases where I’ve seen that happen sometimes it can be avoided by having the calcarine sulcus cut not extend too far around the occipital pole (i.e., slightly shorter cut length), but it definitely varies from case to case. Similarly, on the other end you can try placing the “360” cut which separates the occipital patch from the rest of the cortex slightly more posterior, effectively shortening the calcarine sulcus cut as well.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nasr, Shahin,Ph.D. shahin.nasr@mgh.harvard.edu Date: Tuesday, April 11, 2023 at 7:15 PM To: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution Correct Luis. But I am not sure why did verion 7 act like this.
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/12xWEgEY6hOhhRr7g5fWPK3Gf1dlyz58ha7Pb66KkuhCHkQ...https://secure-web.cisco.com/1dieRkuIGIwcoRKWXF1_E_U5H9RTe-srddJwMy53L6NZ99mla3wO9cZVqA_xvpkRlK5tnf4cXkZf1NKdR1_ltL10ZzVSeOPKzMyIBPh1kofJJtFHEVT5I2FCnNosetA3BEbK-cKZRySjCcio2Ea50puCt1Qet7h12dU4XO_4OCOP4tSp37YJ69LhDU_hA0vSp1ed7nRWv8oJKYKXMPjbNdEjEGcedyz4gugPXAUIs-dq0cse0XeJcDRZW32G2e_AOlz8mKMXrDrpRpsXZppe_xw/https%3A%2F%2Fmesovision.martinos.org%2F ________________________________ From: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Tuesday, April 11, 2023 6:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Subject: RE: mris_flatten Version 6 vs. 7
Thanks Louis! Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Vinke, Louis N.,PHD Sent: Tuesday, April 11, 2023 6:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
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I think it’s just a slight overlap of the flat map. In the FS6 version, using the sulcal pattern as a reference you can see that the calcarine cut does go all the way to that point/vertex. If you were to select two vertices on either side of the “bridge” and make a path, the path would curve around instead of cutting straight across.
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Date: Saturday, April 8, 2023 at 4:34 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>, freesurfer (freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu) <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
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Moving the thread back to the list as I don’t know, but maybe someone else does?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 4:10 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
it doesn't exist in the cut, and I do not see it in the outcome of version 6 (attached).
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 12:02 PM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Subject: RE: mris_flatten Version 6 vs. 7
Oh, looks like you had a small cut there
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 12:02 PM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
In the attached file, I zoomed in and enlarged the location so you can see the issue.
Regards
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 11:54 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Sorry, I don’t see what black dot you are referring to. As for being different, when the distances it uses are random it will change run to run. Basically you hope some of them prevent the patch from folding on itself (which it will definitely be prone to if the distances are only nearest neighbor)
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: mris_flatten Version 6 vs. 7
Hi Bruce,
Adding -distance 20 20 definitely helped (see the attached file). Even though, the outcome is still different than what we see based on Version 6 (my previous emails), which might be OK. But do you notice the black dot (missing vertex) at the tip of calcarine sulcus? Any idea why that is happening? Any solution for that?
Regards,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: RE: mris_flatten Version 6 vs. 7
Can you try running it with -distances 20 20 added to the command line?
From: Nasr, Shahin,Ph.D. <shahin.nasr@MGH.HARVARD.EDUmailto:shahin.nasr@MGH.HARVARD.EDU> Sent: Saturday, April 8, 2023 8:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto: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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
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________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:21 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mris_flatten Version 6 vs. 7
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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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freesurfer@nmr.mgh.harvard.edu
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