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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 https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl...
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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
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/1P3aVCMLKHb_BLyWvymhqZgLdoJeNuAWcgw4ezfIWgyu2I_...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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
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://mesovision.martinos.org/https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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.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
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://mesovision.martinos.org/https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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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/10Bp-Gnq6wu6SRUY9toFujnn8rJe2MhXKbnLznH4AdJdAia... ________________________________ 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.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/10Bp-Gnq6wu6SRUY9toFujnn8rJe2MhXKbnLznH4AdJdAia...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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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,
Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/1pRhCbkpR48CdU88W3s-FUCjVSW7XDaUyt5P7kgKbRh5hh2... ________________________________ 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/1pRhCbkpR48CdU88W3s-FUCjVSW7XDaUyt5P7kgKbRh5hh2...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
p.s. adding -norand won’t fix the failed flattening, it will just make it repeatable. In my experience (admittedly a long time ago now), adding more distances and longer ranges fixes this problem
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce R.,PHD Sent: Saturday, April 8, 2023 10:15 AM To: Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7
External Email - Use Caution 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://mesovision.martinos.org/https://secure-web.cisco.com/1pRhCbkpR48CdU88W3s-FUCjVSW7XDaUyt5P7kgKbRh5hh23GcuOtJkHufkY5tYZ5YhcX3-o5VzW4rqmtfZTItHf74eKTGISkxFCXDlPsfdvEPTDan4T-bi-80GDJX7VnP8KaVwY0rLBvBVIMJXw4uKkfS3I-wH41l3Zkb16vpAmozVwhDwLzyCaGj5GUnP860Yl3kdg3bRuFiByCrsFNdfmhUqTf4jnOKdveWil9U7Wct_90w4xRz0kQrnM1slDR/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
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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/1esWcVSHCPv20Vfn3CxTpnjWeZ200va0QGU_p218umU1Hh1... ________________________________ From: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu Sent: Saturday, April 8, 2023 10:14 AM To: Nasr, Shahin,Ph.D. shahin.nasr@MGH.HARVARD.EDU; Freesurfer support list 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.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,
Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
https://secure-web.cisco.com/1esWcVSHCPv20Vfn3CxTpnjWeZ200va0QGU_p218umU1Hh1...
________________________________
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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1esWcVSHCPv20Vfn3CxTpnjWeZ200va0QGU_p218umU1Hh1...https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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.EDU Sent: Saturday, April 8, 2023 11:47 AM To: Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu; Freesurfer support list 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://mesovision.martinos.org/ ________________________________ 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://mesovision.martinos.org/
________________________________
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://mesovision.martinos.org/https://secure-web.cisco.com/1KKZlmmfbSaMq_e7vZdb7bVOx0Po2Sy-YscOPY5REFynzcl9ogZOQkJt6HiC9xRQgj1PgIK4EZE3_QRhf8lrCWDZ60kS1VzAqauCguAnPFVoVtr3jkuFoQ4Zw_Dh0KMp7wkzfb63kU-dz7Q0bKRt8HXdq5ArZsE3eE59s7tbycEZVEv6UlgzMThQjLUajlJXnV9w39MmHDbjykunqQpHQhkmA-iDu_rLXOsGAJKX31GmzCDMiP9tDgjlvRH1-SKd4vXJzx8Uu-9Z2OCdB0FKSDw/https%3A%2F%2Fmesovision.martinos.org%2F
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