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