External Email - Use Caution Hi Douglas,
Here is the command line: mri_glmfit \ --y rh.thickness-rate.MyStudy.10.mgh \ --fsgd FSGD/MyStudy.fsgd dods\ --C Contrasts/Case-Control_age_gender_race_etiv.mtx\ --surf fsaverage rh \ --cortex \ --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \ --eres-save Also error message in terminal: gdfRead(): reading FSGD/MyStudy.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/1NHVxBIRnha6EjEdEho81-VE9d-vjJ6ivzt10z28vhX9c94pCwosQpkLG4Hfu3nLYp7KMDne5wAk9mK45YIQJEZBe6UlteF2wwLohmZJzp070UjHvv6fqugRAkgBk0uNO3Fsgo5BzblW95J5iO5sXWwZLK-LGAZJJTBaU7mLTkO5L70JRSscCW3pdc-G5KchZMbVyeY65gGH4w5MMIYBSVHvX03spMjZ85XkHbkgYYmWXTFnzqUGhqGgHygP5sLeR7OWPKIzEb7X3pHi7POf0UyEHJAZpQLU9bgT2BnOcClt0kW4mll1ODQDC2Y0U7-0f/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base Variable 2 has character string Female Variables should be continuous numbers FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input Also attached FSGD file below. Thank you so much for the help! Best, Zeng On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > please send your command line and full terminal output as well as the fsgd > file > > On 11/10/2021 5:12 PM, Zeng, Qi wrote: > > External Email - Use Caution > Hi Freesurfer experts, > > Here, I want to design a simple group comparison (two levels: Case vs. > Control) and also count for 4 covariates (two continuous and two > categoricals). However, the GLM model cannot recognize my discrete > variables. What do you suggest to change? > >> FSDG file: > GroupDescriptorFile 1 > Title MyStudy > Class Control > Class Case > Variables age gender race eTIV > Input sub001_base Control 85 Female White 1350519 > Contrast: > >> Design matrix for Case-Control and regress out the effect of age, > gender, race, and eTIV. > -1 1 0 0 0 0 0 0 0 0 > > Best, > Zeng > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/12U-W_RSiRIJWjQDCBYfqvGXFwFXZQgpm04lVl3v5K0t8IYtpEx5cD1xcltIygwIKmo05cI6l-2nfk9uxFgBdWGoedjfSO3t3_Hbh1NQQDj4gxzchE8QF5shV5fOP8ukCqp6pHmkq140ase4PWm8-1key4YN4H_tSk9Wh09gbrQK4nERYcXWQYw8fkpCXcQ3U5MXxTyPgoKWJY68te_B_XbFVhWWhzaz65RTcy1JyJlfZLY6Nyv0LACWWHmWU4NzLmBeHSMh8lssnATJq77P16Tl72f8QkK6_lB_cDhEWqJocd9RxUL3qeDAwtK9UbRCY/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 > http://secure-web.cisco.com/1YGeBpazeZXSLfsCEO4_vE11nUNbtdYgN2Tpx1anls1heh4xx3r9SAPXdptyAb3NQFEWW_wDyFNgmJO__d_VUJ4ZoDc6uOlHryomgspKnDLXlJUxYcwmHguKWwgYZamww28y60Aeq0gJLeaCWbwoahgMRrH8-z5ta2ABmTVYMWcGgKuwlAOzE5hf9artWSY3R9z36qyZBlqSphIF6fAWzYMk0dO_RcNVOZUxOpurwkn6dbDtArOd-sJXNda8_EWB9OYHZ2g5P_tcrpodvlf-MKZGF3VZ3bJH8C4OO5j6Di85pQ4alax7KCxKTYsi_o7YJ/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. > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
MyStudy.fsgd
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