can you send the fsgd file?
Vina Goghari wrote:
Yes I have a Variable line: "Variable Age Sex Scanner," before I list all the Inputs.
Douglas N Greve wrote:
did you declare the variables in the fsgd file? See the examples in the link below.
doug
Vina Goghari wrote:
Hello, I have been trying to follow FreeSurfer guidelines to set up the analysis. I keep getting an error that I'm not sure what I did wrong. If you could take a quick look that would be great! I have qcached the data and run mri-preproc.
mri_glmfit \
--y lh.MERIT_sMRI.thickness.10.mgh \
--fsgd MERIT_sMRI.fsgd dods\
--C lh-con-rel.mtx \
--surf fsaverage lh \
--cortex \
--glmdir MERIT_sMRI.glmdir
This is my error:
shell loop% --y lh.MERIT_sMRI.thickness.10.mgh \ shell loop% --fsgd MERIT_sMRI.fsgd dods\ shell loop% --C lh-con-rel.mtx \ shell loop% --surf fsaverage lh \ shell loop% --cortex \ shell loop% --glmdir MERIT-sMRI.glmdir gdfReadHeader: reading MERIT_sMRI.fsgd INFO: ignoring tag Variable ERROR: gdfReadV1: Input line 1, subjid = MERIT_001 Found 3 variables, expected. 0 FSGDF Format Error: file = MERIT_sMRI.fsgd, tag=Input
Thanks so much!
Douglas N Greve wrote:
Vina, there's an example here which is pretty close to what you are asking https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
Vina Goghari wrote:
Thanks Nick. Would coding the data by elements/label GroupGenderHandedness be equivalent to looking at group effect and then covarying for gender and handedness?
Thanks!
Nick Schmansky wrote:
Vina,
Qdec still doesnt support more than four variables, but you can still do the analysis by manually creating the input files to mri_glmfit by following this tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Nick
On Sun, 2009-02-01 at 20:00 -0600, Vina Goghari wrote:
> Hello Freesurfer group, > I have a couple of questions - I'm using FreeSurfer 4.0.3 to > recon-all my data. I've started using Qdec and I realized that > it won't accept more that 4 variables to be selected. I would > like diagnosis to be my main variable and then age, gender, and > scanner version as covariates. > > Do you know if there is a different version of Qdec that would > allow me to do that analysis and if it is a problem to use data > processed with a different prior version with it? > > Thanks, > Vina > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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