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 CautionDear 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.