Re: [Freesurfer] Unknown problem with fsgd file
The problem is that the class name exceeds the maximum number of characters. For some strange reason I set that to be 50 and the class name is 55. I've changed it in our code tree, but you'll just have to shorten the name and it should work. doug On 10/29/2014 07:15 PM, Bronwyn Overs wrote: > 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 >
[Freesurfer] Unknown problem with fsgd file
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
