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Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error:
"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3
I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much!
*milly mc *
*"Life is a foreign language; all mispronounce it." * *Christopher Morley*
Can you send the command line, all the terminal output, and your fsgd file?
On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:
External Email - Use Caution
Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error:
"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3
I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much!
/milly mc / / / /"Life is a foreign language; all mispronounce it." / /Christopher Morley/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Douglas, Thank you for your reply. Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0 0]/3 As well as the code I am running and the whole output from the terminal.
Thank you so much for your help!
On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the command line, all the terminal output, and your fsgd file?
On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:
External Email - Use CautionHi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error:
"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3
I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much!
*milly mc *
*"Life is a foreign language; all mispronounce it." * *Christopher Morley*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Can you send /data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx ? How did you create this file? A lot of word processors will add special characters that can cause a read failure.
On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:
External Email - Use Caution
Hi Douglas, Thank you for your reply. Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0 0]/3 As well as the code I am running and the whole output from the terminal.
Thank you so much for your help!
On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the command line, all the terminal output, and your fsgd file? On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast" I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3 I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much! /milly mc / / / /"Life is a foreign language; all mispronounce it." / /Christopher Morley/ _______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/15w19HcLKdD4B1_vBlmcXD4oL-M6RdXn_F2Thv6otUqOC9Nj_WEM-KvcS3aSGnoPNXyCu4hoH188ynCVzpYkzfbYZBPcFTwh9xqg2HvCMJkt3WjanO6QvVaz0tIwF8_ZWGa4PgK5KGjwyzFwFkXqOnaSRT1QdZWER4ngYUo4rKVUawKgCZtBSj0tUDmR8R_6ykcQYHvlZmEe8pa8Nk-4-C4sN7toLTgiMCXsci03VxIAxV2x9LhMnwC21vfPMvNr4o8CmZZxPkO4ZCdzNzteI_q9Dnm5cUsuiKUKhqPIFotTolbILGxhT6ur14yaojlHUTthPcdFGxVNqt7CL9r4KcA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/15w19HcLKdD4B1_vBlmcXD4oL-M6RdXn_F2Thv6otUqOC9Nj_WEM-KvcS3aSGnoPNXyCu4hoH188ynCVzpYkzfbYZBPcFTwh9xqg2HvCMJkt3WjanO6QvVaz0tIwF8_ZWGa4PgK5KGjwyzFwFkXqOnaSRT1QdZWER4ngYUo4rKVUawKgCZtBSj0tUDmR8R_6ykcQYHvlZmEe8pa8Nk-4-C4sN7toLTgiMCXsci03VxIAxV2x9LhMnwC21vfPMvNr4o8CmZZxPkO4ZCdzNzteI_q9Dnm5cUsuiKUKhqPIFotTolbILGxhT6ur14yaojlHUTthPcdFGxVNqt7CL9r4KcA/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* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1NMGvDBqKIb3M5Ip7sMKmgiUlq0cnhEJrMe3vJPWhjSf02lAyu9AMGC0YnDWVsSKPnXGwdM4ymwmrfjBiYhOTXQsmT9sSx3AzYn5WogPG_S9Heo5PL9zqCK_ghUHxldgWBcUF0Y5dBkqncGOXzcMyKN73jKNV5bZnQF3qqtJ_IOZnjy1K-m15RJ0uXUWfMb9Qab4qt_tphX705Z6TbZ_nNzlVitMfJALnIzoOO4NqBZrxod7yv_jeCo4wn9qS3UXXqwdN3LcqLWsbGsrgYmH5Js4TsLxBRHN0Mztu3r-ZD6gd6D_37pqZIaOThJ6UiwP1CrAqcgJNEzsbqdqk_oAhWw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1NMGvDBqKIb3M5Ip7sMKmgiUlq0cnhEJrMe3vJPWhjSf02lAyu9AMGC0YnDWVsSKPnXGwdM4ymwmrfjBiYhOTXQsmT9sSx3AzYn5WogPG_S9Heo5PL9zqCK_ghUHxldgWBcUF0Y5dBkqncGOXzcMyKN73jKNV5bZnQF3qqtJ_IOZnjy1K-m15RJ0uXUWfMb9Qab4qt_tphX705Z6TbZ_nNzlVitMfJALnIzoOO4NqBZrxod7yv_jeCo4wn9qS3UXXqwdN3LcqLWsbGsrgYmH5Js4TsLxBRHN0Mztu3r-ZD6gd6D_37pqZIaOThJ6UiwP1CrAqcgJNEzsbqdqk_oAhWw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . 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.-- /milly mc / / / /"Life is a foreign language; all mispronounce it." / /Christopher Morley/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Douglas, thank you for the reply. I am attaching it here. I usually create it (using BASH) as such: << echo “1 -1” > File_Name.mtx and have never had issues, however I have not used "[ ] " on my contrasts before... Thank you so so much for your willingness to help and your time!
On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send /data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx ? How did you create this file? A lot of word processors will add special characters that can cause a read failure.
On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:
External Email - Use CautionHi Douglas, Thank you for your reply. Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0 0]/3 As well as the code I am running and the whole output from the terminal.
Thank you so much for your help!
On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the command line, all the terminal output, and your fsgd file?
On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:
External Email - Use CautionHi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error:
"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3
I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much!
*milly mc *
*"Life is a foreign language; all mispronounce it." * *Christopher Morley*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1EhS5mLd3vSAmlNCDxtorEp_PeqLi4Tso1tegCTjVmHIkFs... https://secure-web.cisco.com/15w19HcLKdD4B1_vBlmcXD4oL-M6RdXn_F2Thv6otUqOC9Nj_WEM-KvcS3aSGnoPNXyCu4hoH188ynCVzpYkzfbYZBPcFTwh9xqg2HvCMJkt3WjanO6QvVaz0tIwF8_ZWGa4PgK5KGjwyzFwFkXqOnaSRT1QdZWER4ngYUo4rKVUawKgCZtBSj0tUDmR8R_6ykcQYHvlZmEe8pa8Nk-4-C4sN7toLTgiMCXsci03VxIAxV2x9LhMnwC21vfPMvNr4o8CmZZxPkO4ZCdzNzteI_q9Dnm5cUsuiKUKhqPIFotTolbILGxhT6ur14yaojlHUTthPcdFGxVNqt7CL9r4KcA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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-- *milly mc *
*"Life is a foreign language; all mispronounce it." * *Christopher Morley*
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You can't put math or brackets in the contrast file. Just use .333 .333 .333 -.333 -.333 -.333 0 0 0 0
On 11/16/2023 10:50 AM, Ludmila Midrigan wrote:
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Dear Douglas, thank you for the reply. I am attaching it here. I usually create it (using BASH) as such: << echo “1 -1” > File_Name.mtx and have never had issues, however I have not used "[ ] " on my contrasts before... Thank you so so much for your willingness to help and your time!
On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send /data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx ? How did you create this file? A lot of word processors will add special characters that can cause a read failure. On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:External Email - Use Caution Hi Douglas, Thank you for your reply. Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0 0]/3 As well as the code I am running and the whole output from the terminal. Thank you so much for your help! On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: Can you send the command line, all the terminal output, and your fsgd file? On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast" I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3 I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much! /milly mc / / / /"Life is a foreign language; all mispronounce it." / /Christopher Morley/ _______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/15w19HcLKdD4B1_vBlmcXD4oL-M6RdXn_F2Thv6otUqOC9Nj_WEM-KvcS3aSGnoPNXyCu4hoH188ynCVzpYkzfbYZBPcFTwh9xqg2HvCMJkt3WjanO6QvVaz0tIwF8_ZWGa4PgK5KGjwyzFwFkXqOnaSRT1QdZWER4ngYUo4rKVUawKgCZtBSj0tUDmR8R_6ykcQYHvlZmEe8pa8Nk-4-C4sN7toLTgiMCXsci03VxIAxV2x9LhMnwC21vfPMvNr4o8CmZZxPkO4ZCdzNzteI_q9Dnm5cUsuiKUKhqPIFotTolbILGxhT6ur14yaojlHUTthPcdFGxVNqt7CL9r4KcA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/15w19HcLKdD4B1_vBlmcXD4oL-M6RdXn_F2Thv6otUqOC9Nj_WEM-KvcS3aSGnoPNXyCu4hoH188ynCVzpYkzfbYZBPcFTwh9xqg2HvCMJkt3WjanO6QvVaz0tIwF8_ZWGa4PgK5KGjwyzFwFkXqOnaSRT1QdZWER4ngYUo4rKVUawKgCZtBSj0tUDmR8R_6ykcQYHvlZmEe8pa8Nk-4-C4sN7toLTgiMCXsci03VxIAxV2x9LhMnwC21vfPMvNr4o8CmZZxPkO4ZCdzNzteI_q9Dnm5cUsuiKUKhqPIFotTolbILGxhT6ur14yaojlHUTthPcdFGxVNqt7CL9r4KcA/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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Douglas N. Greve -
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Ludmila Midrigan