Hi Maria,
That command creates a stack of the percent changes , with one entry per subject (it reduces the longitudinal data of a subject to a single number, e.g. the percent change computed in different ways).
Make sure you know what the difference is between pc1, pc1fit (in your case this is the same , as you only have two time points, so the linear fit will go through the two time points), rate, and SPC. I would recommend to use spc as it is symmetric.
The -osgd tells GLMFIT that we have a single group and we look for difference from zero (of the slope/percent change of aseg volumes).
So instead of it you can pass --fsgd ... --C ... as in a usual analysis. (You should be familiar with fsgd and glmfit, how it is used in a standard cross sectional analysis, take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis which is mainly for surface data, but you get the idea. If you have questions about glmfit, change the subject title of your email to e.g. "question about glmfit with tables"
so that the right people will read the question.
Best, Martin
On 05/17/2017 12:55 AM, Maria A Infante wrote:
Hi
I run the commands listed below and I was wondering if there is a way to get the average pc1 for each group. I get an average for the entire sample. What should I use instead of --osgm?
long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 --do-spc --time years --stack-rate ./qdec/long_3groups.aseg-rate.stack.txt --stack-pc1fit ./qdec/long_3groups.aseg-pc1fit.stack.txt --stack-pc1 ./qdec/long_3groups.aseg-pc1.stack.txt --stack-spc ./qdec/long_3groups.aseg-spc.stack.txt
mri_glmfit --osgm --glmdir long_3groups.aseg-pc1 --table ./qdec/long_3groups.aseg-pc1.stack.txt
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