Dear Freesurfer Mailing list,
I have been attempting to run mri_glmfit using a complicated fsgd file
(1 categorical varible with 5 levels, 3 categorical variables with 2
levels, age as covariate). When I run the command, I receive the
following error:
gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd
Input line 5, subjid = 100121, class
siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined
FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input
I have double checked the fsgd file and confirmed that the class for
participant 100121 was specific correctly at the beginning of the file
(correct spelling and case was used). So I cannot identify the source
of the error. Can you advise me as to what may be going wrong?
My full fsgd file begins like this (I have 389 subjects but have
provided only the first 20 for brevity):
GroupDescriptorFile 1
Title GLM_SiteGender
Class siteBrisbane-anyProtNoProt-genderMale-groupCase
Class siteBrisbane-anyProtNoProt-genderFemale-groupCase
Class siteBrisbane-anyProtNoProt-genderMale-groupControl
Class siteBrisbane-anyProtNoProt-genderFemale-groupControl
Class siteBrisbane-anyProtAnyProt-genderMale-groupCase
Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase
Class siteBrisbane-anyProtAnyProt-genderMale-groupControl
Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl
Class siteMelbourne-anyProtNoProt-genderMale-groupCase
Class siteMelbourne-anyProtNoProt-genderFemale-groupCase
Class siteMelbourne-anyProtNoProt-genderMale-groupControl
Class siteMelbourne-anyProtNoProt-genderFemale-groupControl
Class siteMelbourne-anyProtAnyProt-genderMale-groupCase
Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase
Class siteMelbourne-anyProtAnyProt-genderMale-groupControl
Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl
Class siteNewcastle-anyProtNoProt-genderMale-groupCase
Class siteNewcastle-anyProtNoProt-genderFemale-groupCase
Class siteNewcastle-anyProtNoProt-genderMale-groupControl
Class siteNewcastle-anyProtNoProt-genderFemale-groupControl
Class siteNewcastle-anyProtAnyProt-genderMale-groupCase
Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase
Class siteNewcastle-anyProtAnyProt-genderMale-groupControl
Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl
Class sitePerth-anyProtNoProt-genderMale-groupCase
Class sitePerth-anyProtNoProt-genderFemale-groupCase
Class sitePerth-anyProtNoProt-genderMale-groupControl
Class sitePerth-anyProtNoProt-genderFemale-groupControl
Class sitePerth-anyProtAnyProt-genderMale-groupCase
Class sitePerth-anyProtAnyProt-genderFemale-groupCase
Class sitePerth-anyProtAnyProt-genderMale-groupControl
Class sitePerth-anyProtAnyProt-genderFemale-groupControl
Class siteSydney-anyProtNoProt-genderMale-groupCase
Class siteSydney-anyProtNoProt-genderFemale-groupCase
Class siteSydney-anyProtNoProt-genderMale-groupControl
Class siteSydney-anyProtNoProt-genderFemale-groupControl
Class siteSydney-anyProtAnyProt-genderMale-groupCase
Class siteSydney-anyProtAnyProt-genderFemale-groupCase
Class siteSydney-anyProtAnyProt-genderMale-groupControl
Class siteSydney-anyProtAnyProt-genderFemale-groupControl
Variables age
Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23
Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22
Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39
Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30
Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21
Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53
Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58
Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24
Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24
Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21
Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41
Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19
Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26
Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55
Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30
Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39
Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50
Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25
Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35
Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44
The mri_glmfit command I am using is as follows:
mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd
site-gender-group-prothaplotype.fsgd dods --C gender.mtx --C group.mtx
--C haplotype.mtx --C groupXgender.mtx --C haplotypeXgender.mtx --C
groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh
--cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir
--
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the
NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
_______________________________________________
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 Partners Compliance HelpLine at
http://www.partners.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.
