Vina,
Yes, you can download v4.2.0 and continue to use your v4.0.3 data (just dont mix running recon-all -all of future subjects using v4.2.0 with v4.0.3).
You can use the new mri_glmfit-sim utility with your v4.0.3 data.
Nick
On Tue, 2009-02-03 at 19:01 -0600, Vina Goghari wrote:
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 > > > >
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