Thanks for your help. I probably would not have seen that!
I have been working with 4.0.3 FreeSurfer. I don't think there is a mri_glmfit-sim, though it seems that there is a --sim function for mri_glmfit-sim. I'm have trouble figuring out what the code would be exactly to run it.
Alternatively I can just down load the newer version and use that with my processed 4.03 data?
Thanks!!!
Douglas N Greve wrote:
ah, the line should read "Variables" not "Variable"
doug
Vina Goghari wrote:
Yes. Attached. Thanks!
Douglas N Greve wrote:
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 >>>> >>>> >>>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer