I have found the reason for the error: FSGDF Format Error: file =
/Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input
The class should be 1.0 and 0.0, as stated in the fsgd file.
Otherwise, is the process still correct?
BW
Kasper
> -------- Original Message --------
> Subject: problem with fsgd glmfit
> Local Time: 14 August 2017 10:12 AM
> UTC Time: 14 August 2017 8:12 AM
> From: kas...@brejes.com
> To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>
> Dear FreeSurfer,
>
> I would like to do the long. two stage model
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel)
>
> Study design: 2 groups (one control group, one patient group) with gender and
> age as covariates. Each subject was MRI scanned at baseline and 6 weeks
> follow-up. I would like to test the difference in structural measures between
> groups over time.
>
> My problem
> 1. Is the process and setup below correct?
> 2. When i pass the above command under 3) i get an error where it says:
>
> FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd,
> tag=Input
>
> Is there anyone that can help?
>
> I have followed the tutorial:
>
> FIRST STAGE: Preparing the Data - QCACHE is done.
> SECOND STAGE: Option mri_glmfit:
>
> Then i would like to test the difference between groups, and this is were i
> have a hard time following the tutorial.
>
> I looked at the following guide:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis concerning
> Group Analysis using mri_glmfit and i understand that i need to use the
> command below creating my own fsgd file.
>
> 1) Since i have a longitudinal setup, i converted it to a cross-sectional
> steup as you would do if you used the QDEC option. My fsgd file looks as the
> one below. 1 = patients and 0 = controls.
>
> GroupDescriptorFile 1
> Title GroupDiff_Lh_Thickness
> Class 1
> Class 0
> Variables age gender
> Input b101_base 1.0 24.0 1.0
> Input b103_base 1.0 41.0 0.0
> Input b105_base 1.0 22.0 1.0
> Input b206_base 0.0 25.0 1.0
> Input b207_base 0.0 23.0 0.0
>
> 2) To test group difference between groups regressing out the effect of age
> and gender i have made a .mtx file with the following input:
>
> 1 -1 0 0 0 0
>
> 3) Therenext, i ran the following but something is wrong with my fsgd file:
>
> mri_glmfit --y lh.thickness-spc.stack.fwhm15.mgh --fsgd
> GroupDiffLhThickness.fsgd dods --C group.diff.mtx --surf fsaverage lh
> --cortex --glmdir lh_thickness_spc_fwhm15_groupdiff
>
> I hoper there is someone who can help.
> Best wishes
> Kasper Jessen
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