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Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the "--1d" flag. But, I thought that the flag is "required for any along-tract analysis" as stated in your TraculaStatistics instruction and highlighted in the release notes for v7.2 (added 1D capability for mri_glmfit-sim). I would greatly appreciate for your further clarifications. Thank you so much for your help.

Best regards, Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

Hi Taka - Does it work when you remove the "--1d" from the command line? I think that must be an error in the documentation.

Anastasia.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi < takatr@gmail.com> *Sent:* Wednesday, January 12, 2022 7:04 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

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Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/14xTl-nXfhrT5s1HVQuP9A9vkMOy3hcNKfB2a4mLefQS6dl... https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics). But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 1000 1.3 pos Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac machine with macOS 12.1. Thank you so much for your help.

Sincerely, Taka _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1c51EnIhRXtzkHburMSaQUmVRU0BIZ6uq-xugQ3xdPrY67Z... 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 http://secure-web.cisco.com/1y8tm5nemVBxe3PYik6D1CXDssoJlAY62qadNY4ruULTuoLF... . 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.

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Dear Dr. Yendiki,

Thank you so much for this additional explanation. It’s clear now.

Best regards, Taka

2022/01/21 2:13、Yendiki, Anastasia AYENDIKI@mgh.harvard.eduのメール:

Yes, the tutorial was written when the 7.2 release was in the last stages of development. What happened between then and the final, released 7.2 was that it now just figures out that the input is 1D by checking the dimensions of the input, so you don't have to specify it on the command line. From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tarumi Takashi takatr@gmail.com Sent: Thursday, January 20, 2022 7:59 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

    External Email - Use Caution        

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the "--1d" flag. But, I thought that the flag is "required for any along-tract analysis" as stated in your TraculaStatistics instruction and highlighted in the release notes for v7.2 (added 1D capability for mri_glmfit-sim). I would greatly appreciate for your further clarifications. Thank you so much for your help.

Best regards, Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote: Hi Taka - Does it work when you remove the "--1d" from the command line? I think that must be an error in the documentation.

Anastasia. From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tarumi Takashi takatr@gmail.com Sent: Wednesday, January 12, 2022 7:04 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

    External Email - Use Caution        

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1MfvOB_RivuZacGakSlQntFiJmL3ek2B3qow_L8RuzHu3IW... But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 1000 1.3 pos Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac machine with macOS 12.1. Thank you so much for your help.

Sincerely, Taka _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JIjyXSqrn8YrXsDtjtj0cK2WrsAOTGEAkFWJvZVr1dC2qH... 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://secure-web.cisco.com/1k-3-r_MrjlGx2tXOpq55YLid6LmRVdQXU5A6ST8MojcEtAP... . 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.edu https://secure-web.cisco.com/1JIjyXSqrn8YrXsDtjtj0cK2WrsAOTGEAkFWJvZVr1dC2qH... 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 http://secure-web.cisco.com/1k-3-r_MrjlGx2tXOpq55YLid6LmRVdQXU5A6ST8MojcEtAP... . 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.