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 >
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GroupDescriptorFile 1 Title MERIT_data Class Scz Class Rel Class Con Variable Age Gender Scanner Input MERIT_001 Con 25 1 1 Input MERIT_002 Rel 46 1 1 Input MERIT_003 Scz 50 1 1 Input MERIT_004 Rel 40 1 1 Input MERIT_005 Scz 49 2 1 Input MERIT_006 Rel 43 2 1 Input MERIT_007 Scz 28 1 1 Input MERIT_008 Con 22 1 1 Input MERIT_009 Con 42 2 1 Input MERIT_010 Con 55 1 1 Input MERIT_011 Scz 39 1 1 Input MERIT_012 Rel 47 1 1 Input MERIT_013 Rel 49 1 1 Input MERIT_015 Scz 49 1 1 Input MERIT_016 Rel 53 2 1 Input MERIT_017 Scz 58 2 1 Input MERIT_018 Con 48 1 1 Input MERIT_019 Scz 43 1 1 Input MERIT_020 Rel 58 2 1 Input MERIT_022 Scz 52 1 1 Input MERIT_023 Rel 53 2 1 Input MERIT_024 Con 49 1 1 Input MERIT_025 Scz 53 1 1 Input MERIT_026 Con 21 2 1 Input MERIT_027 Con 35 2 1 Input MERIT_028 Con 38 2 1 Input MERIT_029 Con 32 1 1 Input MERIT_030 Con 30 2 1 Input MERIT_031 Rel 57 1 1 Input MERIT_032 Con 26 2 1 Input MERIT_033 Con 32 2 1 Input MERIT_034 Scz 33 1 1 Input MERIT_035 Con 42 1 1 Input MERIT_036 Rel 55 2 1 Input MERIT_037 Rel 56 1 1 Input MERIT_038 Scz 36 2 1 Input MERIT_039 Con 47 1 1 Input MERIT_040 Scz 28 1 1 Input MERIT_041 Scz 42 1 1 Input MERIT_043 Scz 52 1 2 Input MERIT_044 Rel 31 2 2 Input MERIT_045 Rel 43 2 2 Input MERIT_046 Scz 41 1 2 Input MERIT_047 Scz 51 1 2 Input MERIT_048 Con 27 2 2 Input MERIT_049 Rel 48 2 2 Input MERIT_050 Scz 42 1 2 Input MERIT_051 Scz 30 1 2 Input MERIT_052 Scz 49 1 2 Input MERIT_053 Scz 54 2 2 Input MERIT_054 Rel 58 2 2 Input MERIT_055 Con 42 1 2 Input MERIT_056 Scz 58 1 2 Input MERIT_057 Con 27 1 2 Input MERIT_058 Scz 44 2 2 Input MERIT_059 Con 23 1 2 Input MERIT_060 Scz 59 1 2 Input MERIT_061 Con 58 1 2 Input MERIT_062 Con 49 2 2 Input MERIT_063 Scz 35 2 2 Input MERIT_064 Con 44 2 2 Input MERIT_065 Con 44 2 2 Input MERIT_067 Scz 40 1 2 Input MERIT_068 Rel 55 2 2 Input MERIT_069 Con 53 1 2 Input MERIT_070 Rel 53 2 2 Input MERIT_071 Con 50 2 2 Input MERIT_072 Rel 51 1 2 Input MERIT_073 Con 49 2 2 Input MERIT_074 Scz 22 1 2 Input MERIT_075 Rel 52 2 2 Input MERIT_076 Rel 44 2 2 Input MERIT_077 Scz 36 1 2 Input MERIT_078 Con 56 1 2 Input MERIT_079 Con 59 2 2 Input MERIT_080 Con 52 1 2 Input MERIT_081 Con 47 2 2 Input MERIT_082 Con 53 1 2 Input MERIT_083 Con 52 1 2 Input MERIT_084 Rel 50 2 2 Input MERIT_085 Rel 53 2 2 Input MERIT_086 Con 51 1 2 Input MERIT_087 Con 40 1 2 Input MERIT_088 Con 57 1 2 Input MERIT_089 Con 40 2 2 Input MERIT_090 Rel 50 1 2