I would advice setting up the FSGD files with 8 classes based on your 3
discrete, 2-level variables, eg, MaleControlWhite then use two
continuous variables Age and eTIV.
You should definitely normalize the eTIV (and probably age too)
On 11/10/2021 7:07 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Douglas,
Just to be clear, should I recode discrete variables as numeric as
sample1) or change discrete variables into strings 2) or even change
the comparison groups into strings too 3)?
1)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85111350519.71
InputSub002_baseControl81.3 011558515.86
InputSub003_baseControl81.3 001558515.86
or 2)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85"Female""White"1350519.71
InputSub002_baseControl81.3 "Male""White"1558515.86
InputSub003_baseControl72.7 "Male""White"1187649.47
or 3)
Variables AgeGenderRaceeTIV
InputSub001_base"Control"85"Female""White"1350519.71
InputSub002_base"Control"81.3 "Male""White"1558515.86
InputSub003_base"Control"72.7 "Male""White"1187649.47
Best,
Zeng
On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
Did you read the error message? It says:
Variable 2 has character string Female
Variables should be continuous numbers
You have listed Gender and Race as strings, they have to be
numbers (eg, 1, 2)
You probably want to have these be discrete variables instead of
continuous
On 11/10/2021 6:20 PM, Zeng, Qi wrote:
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 *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
<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 agegenderrace eTIV
Inputsub001_baseControl85FemaleWhite1350519
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 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/12U-W_RSiRIJWjQDCBYfqvGXFwFXZQgpm04lVl3v5K0t8IYtpEx5cD1xcltIygwIKmo05cI6l-2nfk9uxFgBdWGoedjfSO3t3_Hbh1NQQDj4gxzchE8QF5shV5fOP8ukCqp6pHmkq140ase4PWm8-1key4YN4H_tSk9Wh09gbrQK4nERYcXWQYw8fkpCXcQ3U5MXxTyPgoKWJY68te_B_XbFVhWWhzaz65RTcy1JyJlfZLY6Nyv0LACWWHmWU4NzLmBeHSMh8lssnATJq77P16Tl72f8QkK6_lB_cDhEWqJocd9RxUL3qeDAwtK9UbRCY/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/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 *MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be*
http://www.massgeneralbrigham.org/complianceline
<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
_______________________________________________
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/1riDKYS-FGseRCaBPDFbfM10KeLQ0kNrmsbKoEpOzznltcGj9v-5n_mtcH4iuPpyQdPnJpDqv2oznuvHcCG0AoePAHtplLU3aqtaLbpH7r9l72LUZMShuoVRoexJpk22Z0KJ4UF-qkQIfw_bIfhHlkLc9H1-DLhctPeXE_toredYS7-4qs-W0QxiUq1kBtbAmLnJmze-ioLsfDBZDMhUGZSIqNcc_nJSQEFuPObCRfGVv7Y_ezTrjPIZOHsEOd76lP4BnUE2VlZRnW0o0mGf6V2ypN9V9CJ1uEZL6XvCbunFWu-JldhQmq1KCGRlJsi29A0RAnLJ_ZCLu878-nqCy4A/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/1riDKYS-FGseRCaBPDFbfM10KeLQ0kNrmsbKoEpOzznltcGj9v-5n_mtcH4iuPpyQdPnJpDqv2oznuvHcCG0AoePAHtplLU3aqtaLbpH7r9l72LUZMShuoVRoexJpk22Z0KJ4UF-qkQIfw_bIfhHlkLc9H1-DLhctPeXE_toredYS7-4qs-W0QxiUq1kBtbAmLnJmze-ioLsfDBZDMhUGZSIqNcc_nJSQEFuPObCRfGVv7Y_ezTrjPIZOHsEOd76lP4BnUE2VlZRnW0o0mGf6V2ypN9V9CJ1uEZL6XvCbunFWu-JldhQmq1KCGRlJsi29A0RAnLJ_ZCLu878-nqCy4A/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/complianceline
<http://secure-web.cisco.com/1A0Ya5XLTopPJxtvY6W3BYdLWR_an51gQ8KKFgKuexXEwHqDE7UducPFqwa4W_f6drzqLO6TTfvJdl9TX8bb_Bun8KQdoN6jifg--1DaRPgK5vpDhmxdsEcl2bKSctpeFFx0GwtqNMhTRicmYN40mg6ODHXYoyJ1-uEoIcYfMbwV9kaf7Ggw7BjK35YGkFlfgKF0yB34izSkUcV650w8LfbSh3JDpiyby-RAkFWfC4xGWVUx456s63epPX2GtYCYeK0dWrdSxnJ5k_P7HsJkMjsgcVyRxWcP1EKJr322sUOkeAGLe3Oi_nxkSIy5LtzFFPkR_jNJ2FYtT4NHHqEgTvg/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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline . 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.
