Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

thanks, Ali _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lWS7k_9IBbZ2R5wLwnXky72Hvb1IPtM8sLkLYEGXldiPpYbvdN7xfKq014rZUSlhI16W60bEvOd-TPBjG7v2erPwGsF2O15iWHEC-QuMcO0RSWQQ26UoKnW_oXRace4lVyt0kbGOtiQsrgT6q32lQ5RU8rHkxWIM1drW0GBMT5R1qWFL72-jNhlzRvKrMBT9MGDXqCzogR4isOCAkjLg9ctCWOMH4KFIWtkyQPsWSjEbLcGDH7za_U01rayTRmWgC0s40onpACi74WOBbog8kzVXexYoVJ-_Zgrct1MR6OeXndsq-OCFc6uhBoeNOLv8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1M19CrSIRyg03r19_FIi_DXpCpNZ8_-6tnYEVeAdoMXaNyDqP62hw3Qt7yluuKBXgM3i3KxlZLTQU3c3qVd-1TvlPK7ObT1D2d5LoQoNN09V74MFa0rshfCdOetnM0VE-8naHMXrK-3OKuq9PE1iANvhE1JEjYr6D5QWhgtg69dDdMkYr4NVjph6H9BKm4-AWuCR2k1jDfpZkH0eRR0DuDK1ylhE7uPXL6bP5Fu29Hy84qeYcaFFtAvYs_5VJdVQCvILnzUm3RDF6WEX2kFzuMclZUXF8M-zp1hT9h3QKrPdMheQHcrZtWIzMNaL3yYPS/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Hi Ali

Can you send us the full command line and output in text?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

thanks, Ali _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lWS7k_9IBbZ2R5wLwnXky72Hvb1IPtM8sLkLYEGXldiPpYbvdN7xfKq014rZUSlhI16W60bEvOd-TPBjG7v2erPwGsF2O15iWHEC-QuMcO0RSWQQ26UoKnW_oXRace4lVyt0kbGOtiQsrgT6q32lQ5RU8rHkxWIM1drW0GBMT5R1qWFL72-jNhlzRvKrMBT9MGDXqCzogR4isOCAkjLg9ctCWOMH4KFIWtkyQPsWSjEbLcGDH7za_U01rayTRmWgC0s40onpACi74WOBbog8kzVXexYoVJ-_Zgrct1MR6OeXndsq-OCFc6uhBoeNOLv8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1M19CrSIRyg03r19_FIi_DXpCpNZ8_-6tnYEVeAdoMXaNyDqP62hw3Qt7yluuKBXgM3i3KxlZLTQU3c3qVd-1TvlPK7ObT1D2d5LoQoNN09V74MFa0rshfCdOetnM0VE-8naHMXrK-3OKuq9PE1iANvhE1JEjYr6D5QWhgtg69dDdMkYr4NVjph6H9BKm4-AWuCR2k1jDfpZkH0eRR0DuDK1ylhE7uPXL6bP5Fu29Hy84qeYcaFFtAvYs_5VJdVQCvILnzUm3RDF6WEX2kFzuMclZUXF8M-zp1hT9h3QKrPdMheQHcrZtWIzMNaL3yYPS/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ghRhx-nX9P_DcnD2SaLRclIR7k1Wmcmpukp8rGp7ZHZNTCVfIYzPCytS_FWa-MqqGueLqfYuqwhvenO3VqbgbKzHZMDM9pH5yH41ikB7t8b1EOSqfms17FJBaXiM9hsb59BaYfNoKiYPjSTmZuE5JNDIGNauTyNqwWuTvzWVLHUYFPgK412E-SwUtEdO_0wBYtf2w-ZzXpPlT6mRvd0cojdYNRTFi_Yd_2DGcJO4KwTbtBmTjxTqUwiiEbceaGYvwc0alFWewADakiVm9mLTMPw3S9BfyucSt7zYjFLXuTH7VaXtsVbaYla7DEdd6MMu/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1JDAl8Z0nF7QP8ahs9a3MCk1Rna2C5gk1ujHnbR3soXBHMbOMOSqwNAAGpi_gMYm-UbdyfL-3R1G13sdyenH8s5lcJUSYlssX4z5M2q3T2KJiQ29p5rX2ZR-9Nu9XuSZoaI2VgEJ6sP5ofv5H27_L59Cxm8uZDPmie9EB8CVfjfsHwgNV4ipmNoGWVai7EH61Moyizql38cuteiVnQLLTbclkDDViDWTnX9Kyn8VPYZAefds0N6Od-V1fnC7LMM6pkhVuEwZQ_qMdKyMOj1nDtaKsnt8DdPOr9xb4cR5F_--eF2IM8zhafpAgGIwzc35n/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated

output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed

On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in text?

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 Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

thanks, Ali _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lWS7k_9IBbZ2R5wLwnXky72Hvb1IPtM8sLkLYEGXldiPpYbvdN7xfKq014rZUSlhI16W60bEvOd-TPBjG7v2erPwGsF2O15iWHEC-QuMcO0RSWQQ26UoKnW_oXRace4lVyt0kbGOtiQsrgT6q32lQ5RU8rHkxWIM1drW0GBMT5R1qWFL72-jNhlzRvKrMBT9MGDXqCzogR4isOCAkjLg9ctCWOMH4KFIWtkyQPsWSjEbLcGDH7za_U01rayTRmWgC0s40onpACi74WOBbog8kzVXexYoVJ-_Zgrct1MR6OeXndsq-OCFc6uhBoeNOLv8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1M19CrSIRyg03r19_FIi_DXpCpNZ8_-6tnYEVeAdoMXaNyDqP62hw3Qt7yluuKBXgM3i3KxlZLTQU3c3qVd-1TvlPK7ObT1D2d5LoQoNN09V74MFa0rshfCdOetnM0VE-8naHMXrK-3OKuq9PE1iANvhE1JEjYr6D5QWhgtg69dDdMkYr4NVjph6H9BKm4-AWuCR2k1jDfpZkH0eRR0DuDK1ylhE7uPXL6bP5Fu29Hy84qeYcaFFtAvYs_5VJdVQCvILnzUm3RDF6WEX2kFzuMclZUXF8M-zp1hT9h3QKrPdMheQHcrZtWIzMNaL3yYPS/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ghRhx-nX9P_DcnD2SaLRclIR7k1Wmcmpukp8rGp7ZHZNTCVfIYzPCytS_FWa-MqqGueLqfYuqwhvenO3VqbgbKzHZMDM9pH5yH41ikB7t8b1EOSqfms17FJBaXiM9hsb59BaYfNoKiYPjSTmZuE5JNDIGNauTyNqwWuTvzWVLHUYFPgK412E-SwUtEdO_0wBYtf2w-ZzXpPlT6mRvd0cojdYNRTFi_Yd_2DGcJO4KwTbtBmTjxTqUwiiEbceaGYvwc0alFWewADakiVm9mLTMPw3S9BfyucSt7zYjFLXuTH7VaXtsVbaYla7DEdd6MMu/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1JDAl8Z0nF7QP8ahs9a3MCk1Rna2C5gk1ujHnbR3soXBHMbOMOSqwNAAGpi_gMYm-UbdyfL-3R1G13sdyenH8s5lcJUSYlssX4z5M2q3T2KJiQ29p5rX2ZR-9Nu9XuSZoaI2VgEJ6sP5ofv5H27_L59Cxm8uZDPmie9EB8CVfjfsHwgNV4ipmNoGWVai7EH61Moyizql38cuteiVnQLLTbclkDDViDWTnX9Kyn8VPYZAefds0N6Od-V1fnC7LMM6pkhVuEwZQ_qMdKyMOj1nDtaKsnt8DdPOr9xb4cR5F_--eF2IM8zhafpAgGIwzc35n/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1D2zS-T9qfCgilerdjsj5vdhrzax4yQHB3n5CwpsXfNjUDJ2VD2dcQTcp-bCIIx3CR3ztSi4Ot8EcWfxR9jAlcDXJihQFk4pYb-6dpSzw1Z6aW871PK7vsRuChWO6Lyez757VpHWxokPtH_AiCWpH8Q3TDW-UbFoDcwlAXrlpso70SKygXTKArAKBiwk6a0bMAg2Or-uFtY529cFTnWpgv7S3bak8DTcerE9hdFBp9yLT7JtIT2jfMqOi_dFd1UlNXEereT7eDj8SP948SNaeCZEZ5HPW6aZIi4qE6ngGFC_-Y2L5kghjLVw-MGWgG63l/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1HbLngS1a_N2ZW9zBpmkIhmccdKVeo-Vbertx5Oir0wTsr9wuIPxEvSePL6TS4UpghI_sO6x55t7U0RySzLVhzoXBZSBCBefTGXv8pUy9tlm6AyaOj7Nid-6_e1Cxm2t-SfAfFdeBU6GC2s2e8VymuLkmcrW7YiTW-j1yWw9uzL1d-Jujg6g7Mx6YcLHnaM7i1b98prDL5LKWtbZ2EwTBduqBraw-b48zerml0q8v3Vf5OCozOaiyPpWJYDbHTKIJu__WaxQTGtvcbrnSyDYdx7Rx9CMLe8QwhukaRN86GLajwXLzb4eKvoWHGf6StJ0n/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

No, it should be:

freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated

the $ means to dereference a variable, so it was trying to find an environment var named IM

cheers Bruce From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 7:01 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution IM-0001 is the subject name. should i instead be doing freeview -f $SUBJECTS_DIR/$subjects/IM-0001 ?

On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?

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 Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated

output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed

On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in text?

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 Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

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It should be displayed by default, but you can also load it by clicking the curvature pulldown menu and then “Reload…”

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 10:30 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Thank you that opened up freeview. When I click file to load the curvature file there ain't an option for it. I need the curvature file to guide the cuts or else it will be an estimation. Any ideas why this would be?

Thanks

On Mon 6 Dec 2021, 15:24 Fischl, Bruce, <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: No, it should be:

freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated

the $ means to dereference a variable, so it was trying to find an environment var named IM

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 Alison McDonnell Sent: Monday, December 6, 2021 7:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution IM-0001 is the subject name. should i instead be doing freeview -f $SUBJECTS_DIR/$subjects/IM-0001 ?

On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?

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 Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated

output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed

On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in text?

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 Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

thanks, Ali _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lWS7k_9IBbZ2R5wLwnXky72Hvb1IPtM8sLkLYEGXldiPpYbvdN7xfKq014rZUSlhI16W60bEvOd-TPBjG7v2erPwGsF2O15iWHEC-QuMcO0RSWQQ26UoKnW_oXRace4lVyt0kbGOtiQsrgT6q32lQ5RU8rHkxWIM1drW0GBMT5R1qWFL72-jNhlzRvKrMBT9MGDXqCzogR4isOCAkjLg9ctCWOMH4KFIWtkyQPsWSjEbLcGDH7za_U01rayTRmWgC0s40onpACi74WOBbog8kzVXexYoVJ-_Zgrct1MR6OeXndsq-OCFc6uhBoeNOLv8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Hi Ali

Can you send us the full command line and output in general? What directory are you running that from? If not the surf dir then you need to include paths to the input and output patches (BTW I wouldn’t name the output “.3D”. Our naming convention is to use .patch as the extension of all of them, and have .3D.patch be the input to mris_flatten and .flat.patch be the output)

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 10:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution I've made the patch and saved it and am now trying to flatten using "mris_flatten lh.full.patch.3D lh.full.flat.patch.3D" but it is giving errors:

error: No such file or directory error: MRISread(/Users/ali/lh.smoothwm): could not open file error: No such file or directory error: mris_flatten: could not read surface file /Users/ali/lh.smoothwm

I can see the lh.full.patch file and smoothwm file in the surf folder.

Thanks

On Mon, 6 Dec 2021 at 15:35, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: It should be displayed by default, but you can also load it by clicking the curvature pulldown menu and then “Reload…”

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 Alison McDonnell Sent: Monday, December 6, 2021 10:30 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Thank you that opened up freeview. When I click file to load the curvature file there ain't an option for it. I need the curvature file to guide the cuts or else it will be an estimation. Any ideas why this would be?

Thanks

On Mon 6 Dec 2021, 15:24 Fischl, Bruce, <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: No, it should be:

freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated

the $ means to dereference a variable, so it was trying to find an environment var named IM

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 Alison McDonnell Sent: Monday, December 6, 2021 7:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution IM-0001 is the subject name. should i instead be doing freeview -f $SUBJECTS_DIR/$subjects/IM-0001 ?

On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?

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 Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated

output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed

On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in text?

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 Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

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So it should be:

mris_flatten $SUBJECTS_DIR/IM-0001/surf/lh.full.patch.3D $SUBJECTS_DIR/IM-0001/surf/lh.full.flat.patch.3D

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alison McDonnell Sent: Monday, December 6, 2021 12:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution The command line is

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

The files are in the surf folder in the IM-0001 subject in subjects. took up this project so am following their naming but will change once i have it working but think it'll get confusing if i change before then

Thanks

On Mon, 6 Dec 2021 at 16:56, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in general? What directory are you running that from? If not the surf dir then you need to include paths to the input and output patches (BTW I wouldn’t name the output “.3D”. Our naming convention is to use .patch as the extension of all of them, and have .3D.patch be the input to mris_flatten and .flat.patch be the output)

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 Alison McDonnell Sent: Monday, December 6, 2021 10:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution I've made the patch and saved it and am now trying to flatten using "mris_flatten lh.full.patch.3D lh.full.flat.patch.3D" but it is giving errors:

error: No such file or directory error: MRISread(/Users/ali/lh.smoothwm): could not open file error: No such file or directory error: mris_flatten: could not read surface file /Users/ali/lh.smoothwm

I can see the lh.full.patch file and smoothwm file in the surf folder.

Thanks

On Mon, 6 Dec 2021 at 15:35, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: It should be displayed by default, but you can also load it by clicking the curvature pulldown menu and then “Reload…”

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 Alison McDonnell Sent: Monday, December 6, 2021 10:30 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Thank you that opened up freeview. When I click file to load the curvature file there ain't an option for it. I need the curvature file to guide the cuts or else it will be an estimation. Any ideas why this would be?

Thanks

On Mon 6 Dec 2021, 15:24 Fischl, Bruce, <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: No, it should be:

freeview -f $SUBJECTS_DIR/IM-0001/surf/lh.inflated

the $ means to dereference a variable, so it was trying to find an environment var named IM

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 Alison McDonnell Sent: Monday, December 6, 2021 7:01 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution IM-0001 is the subject name. should i instead be doing freeview -f $SUBJECTS_DIR/$subjects/IM-0001 ?

On Thu, 2 Dec 2021 at 17:42, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Thanks. What are you expecting from $IM-0001. Is IM a variable? Maybe you just want to remove the $?

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 Alison McDonnell Sent: Thursday, December 2, 2021 10:22 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution command line: freeview -f $SUBJECTS_DIR/$IM-0001/surf/lh.inflated

output at terminal: error: No such file or directory error: MRISread(/Users/ali/freesurfer/subjects/-0001/surf/lh.inflated): could not open file MRISread failed

On Thu, 2 Dec 2021 at 15:00, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the full command line and output in text?

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 Alison McDonnell Sent: Thursday, December 2, 2021 8:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I used the command line you said and freeview opened but gave an error message saying it failed to load the surface but in my folder i have an lh.inflated file.

Thanks, Ali

On Wed, 1 Dec 2021 at 15:05, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

Can you send us the command line and full terminal output as text, not as a snapshot? To open a surface you would do:

freeview -f $SUBJECTS_DIR/$subject/surf/lh.inflated

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 Alison McDonnell Sent: Wednesday, December 1, 2021 4:59 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution Hi Bruce,

I tried to open it using freeview so I could make those cuts but it opened freeview and said couldn't open mri and in the terminal it said it couldn't determine the file type as can be seen in the screenshot I attached in my original email. I don't know why it wouldn't let me open it?

Thanks, Ali

On Tue, 30 Nov 2021 at 20:06, Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Hi Ali

No, there is no auto-cutting. You need to cut your own patch 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 Alison McDonnell Sent: Tuesday, November 30, 2021 2:01 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FREESURFER issue making flatmap

External Email - Use Caution hi all,

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then.

thanks, Ali _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lWS7k_9IBbZ2R5wLwnXky72Hvb1IPtM8sLkLYEGXldiPpYbvdN7xfKq014rZUSlhI16W60bEvOd-TPBjG7v2erPwGsF2O15iWHEC-QuMcO0RSWQQ26UoKnW_oXRace4lVyt0kbGOtiQsrgT6q32lQ5RU8rHkxWIM1drW0GBMT5R1qWFL72-jNhlzRvKrMBT9MGDXqCzogR4isOCAkjLg9ctCWOMH4KFIWtkyQPsWSjEbLcGDH7za_U01rayTRmWgC0s40onpACi74WOBbog8kzVXexYoVJ-_Zgrct1MR6OeXndsq-OCFc6uhBoeNOLv8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1ghRhx-nX9P_DcnD2SaLRclIR7k1Wmcmpukp8rGp7ZHZNTCVfIYzPCytS_FWa-MqqGueLqfYuqwhvenO3VqbgbKzHZMDM9pH5yH41ikB7t8b1EOSqfms17FJBaXiM9hsb59BaYfNoKiYPjSTmZuE5JNDIGNauTyNqwWuTvzWVLHUYFPgK412E-SwUtEdO_0wBYtf2w-ZzXpPlT6mRvd0cojdYNRTFi_Yd_2DGcJO4KwTbtBmTjxTqUwiiEbceaGYvwc0alFWewADakiVm9mLTMPw3S9BfyucSt7zYjFLXuTH7VaXtsVbaYla7DEdd6MMu/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1JDAl8Z0nF7QP8ahs9a3MCk1Rna2C5gk1ujHnbR3soXBHMbOMOSqwNAAGpi_gMYm-UbdyfL-3R1G13sdyenH8s5lcJUSYlssX4z5M2q3T2KJiQ29p5rX2ZR-9Nu9XuSZoaI2VgEJ6sP5ofv5H27_L59Cxm8uZDPmie9EB8CVfjfsHwgNV4ipmNoGWVai7EH61Moyizql38cuteiVnQLLTbclkDDViDWTnX9Kyn8VPYZAefds0N6Od-V1fnC7LMM6pkhVuEwZQ_qMdKyMOj1nDtaKsnt8DdPOr9xb4cR5F_--eF2IM8zhafpAgGIwzc35n/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1D2zS-T9qfCgilerdjsj5vdhrzax4yQHB3n5CwpsXfNjUDJ2VD2dcQTcp-bCIIx3CR3ztSi4Ot8EcWfxR9jAlcDXJihQFk4pYb-6dpSzw1Z6aW871PK7vsRuChWO6Lyez757VpHWxokPtH_AiCWpH8Q3TDW-UbFoDcwlAXrlpso70SKygXTKArAKBiwk6a0bMAg2Or-uFtY529cFTnWpgv7S3bak8DTcerE9hdFBp9yLT7JtIT2jfMqOi_dFd1UlNXEereT7eDj8SP948SNaeCZEZ5HPW6aZIi4qE6ngGFC_-Y2L5kghjLVw-MGWgG63l/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1HbLngS1a_N2ZW9zBpmkIhmccdKVeo-Vbertx5Oir0wTsr9wuIPxEvSePL6TS4UpghI_sO6x55t7U0RySzLVhzoXBZSBCBefTGXv8pUy9tlm6AyaOj7Nid-6_e1Cxm2t-SfAfFdeBU6GC2s2e8VymuLkmcrW7YiTW-j1yWw9uzL1d-Jujg6g7Mx6YcLHnaM7i1b98prDL5LKWtbZ2EwTBduqBraw-b48zerml0q8v3Vf5OCozOaiyPpWJYDbHTKIJu__WaxQTGtvcbrnSyDYdx7Rx9CMLe8QwhukaRN86GLajwXLzb4eKvoWHGf6StJ0n/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1YToNq-oMLs4Iv092qnrFo21prEGaTFKQXOgwbv8cu1R2Ef8l3Orbyr8va47st1zI1IvB5Ai_aakrii8WvRPlqiyJ60jx3M5gULbk0qpblZlsDqCSK__X9psSuSigUow56GS9VyObzqF5YEmNWz3V1JTBLl35f7dSrhrPC-UK9d_--MK7dwO6qfOhWDTcb2pNbBbOyaQ-u5Uke6ViSiT4JVxckTZ2DjLTYmTNhULiEbnVyXaK-S5xzTWaRRKHbEIoD664i8GvbSx3LQMf1oF-lLjgGgMkjdvvOyjF7MyW2eYjXUqV0POzCDb0jQOL--ZY3A3u0f8WaJstmhWvOBln3g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1txZ1RRvCzGNnR3hYBEMmvT1KaXal-x7L0_wofrRbe00UmKp_Jz8WIWeTwRnlxL6KsnXjfs4wtShE-TVw7om5-4JKkMgsA5V5r3helx7Qtam7-JsYVZXSbXOfHb3CG2KlAZ_MAgMSICY9bDOEl4qAqRdzLAKcgt8rxQ7wi3DxKY9g5MDnL-gQbU3LiQN_Dl2F51khsDMOkGiD1iuRt4W5gpVBZS3KZk6ZOUBWiwa1hzXspplrQ5mH7ew9F5kyHHmPmu3JhJGb6k1G0RTh61pSRLziQOuhx9YUqE3U35hds26pCd-QzG5yTFvO6IkrD56_5e6fjf2z2Tqsjw1NU6pXLQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1Wzvm-qZkoxNIgIvjbNOeXErke0Dis0M3PR_zRZz5Nlao5Xg1Rgn138iUE0jCatNB0toZz8c8mldrMlcwcb26SpirFIYzcdZHyo4mHHmqCSHPI8NRqY5br728J32PAlkJTuAvUJv4Rpe__RcXBXTss4JjipIoEQYSBg6PJhDlRc14ylGgo_5L6SmoaigO1QMFmJkfqI6YCfMnNOWC2KRwUOJSeTWt4VWZImNvPlb_TujUYckaCmhKpOTNitHQOyxovfLOr1uaI4jXW-UGdDfuxbbQ0jIWKepD_t7H5bMZYpuy8gceTc-sfLafR5SAYX3F0PrRyp36KRYThd4_DrQH7w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1KkSULnusi0d2eSBAmRN6vFDNfj-3wLnpfMZ4N9mTy7D7PxxLHxUWQJtmJlnM90VyKTP9y0XT1NOI6wLcgeWHsu_lf4YDZFYREzZeokDXxz_f9iSLlYT9ho063lRXW03X7Y3-lagbpnAygBSPKam7MfLwQTND70LZb8_vJQqb4mIimbf5zpJ0fX5dsxzimcTUkF7v1mYxzoT8-6Gv-lAzx3emKwQzFvjyBV5oXb2uWNrwmsuqAHKHV08JvN_nZ-nDFsBFgrxfY4aYniHnS694lmDx0_mnPxqJc1_34Ng6womPjnLP5-2_qEweaFaqdpe51c9rZeYzyz6hoy7ikKGi2A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1Pq1Bk_K89QO_kA6MZhoDxsqWDd1Howf4QyB2db2mXaj-QhcPPTYTje84TnWR8NLMvtYfUAdoR-yJRa9mLgVqX6Z-7cv_ORAP9HgU5cnZ59xIzBcN7dEvLwyY3xXagiK2MC-sf4R7bKGrub2rcOOZG6m2mE0feAYifNKuScjQSVck_8qKCTXuNBmB_f5sugzM0tZuMaev64y-Znbi40d9SNBqIOc0WsZS1sdt-CsG-B6yu5ERmp-OaiqFexZqKmusQ7zdQ6BuHSeKkuFY_eRlPchnvdKfaoEaqY3V1YqAv4W-h5VfDOaDYr_6QBvoVtVKZ2ElrqnNRc3A987HkKQ_0A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1VlzWLLKEoj-FSXu3dbQ0yF2bMqghKBsNczaoHqoVsEPeQTgMjM3AwYAIpoCA5yLjjYg2Fx4y6dMV2_BtPPp8XcPWk2GQlTUIsoqU6KMr61SW_7Usd4KlyPnp6fn6WWBAa2jY1PFaK7ffbtfexI1gJYAn7ON703l7aHuMyKJDDN3v-9tnd_zdMRDVwunpDoDD0u1pTxpIll5bVLzi5eWDKWd7c4LeWe20H-IYo5_oOsLMGpGDfAeejA3nahG9j0wrHzNaUddSXsJy_2GqZHCXv12NA-KhxttuueCSZdPFRBcJp6MPvMFmrFuSNAR8k5jSq4cbMCwWUfeOEzMVx_sv8A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1jMTBdkk0t1zzhObA0tTFo7IBJ5GcChdZWnwdcacH6B6epryz01e6tOBt4WaqrwwPVrVEs8HiNRSrmDVS4-i7koqfn_nhbm-Zm8Xx5Qux3cYd3nAfTMYYR6usoMWMc5u33PSeDc-qjrE0e1PMiUnBSC2pDxDmaJFAYvxgcnfsZVUEIFEL3LsoLl-PETE_0F1p_VCK3g2MeY6oHVq5-_R1Zhf2zh7_biiQLDj19MXvlNUfEsxEKKcQ681NbpJfUQZqpPA1piGCzxI4whsKSX6wsA6NaPx0QyHb4YN0y9Ym6k8G6NyrnoDOqcz4QHqxv8hu/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1gFNFZty-Pdw3TpI-AfkLCr9gi3kJ3O6YVbHnzDAZMJJs_oE3iV0ARVB0d8Fa6dq5smSgGkLu95t3ZgKcg2F-dTf8E6BVU9I0rxD5VOCC4vDtYN_ng69kzYECYk5fx-WV_FBJOSpGSXpS8hOlyIj08i0Ivt8rjbhXBR_3zJxu9vCijC6_Oqaiort9chHh6fGdxqMlG42WeNJJsyYcX0efj6FEbC7O7eD8mTIKBIfmP6vMxW7uOv7pLs2XS-6VVRSthIMCOgUhmeJyMfkqZRuTwvx1OLja_48u1SX0Infadp2uGVqghE2546mj9Q6_AZ8K/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.