Hi Meike,

Would it be possible to send us one of the sig.mgh files to inspect?

Thanks, Ruopeng

On 3/9/20 3:24 PM, Meike Hettwer wrote:

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Dear freesurfer experts,

I am currently running a very basic correlation with two groups (gender, which I am not interested in), age and genetic scores (the latter of which I am interested in) included in the glm. Atm I am using a DODS model (0 0 0 0 0.5 0.5), however, as I am actually not at all interested in gender differences...would it be smarter to use a DOSS model? (0 0 1 ?).

And a question regarding freeview: I always get "failed to load Surface overlay"/"could not open file" errors when trying to overlay calculated sig.mgh (or beta.mgh or pretty much anything) on the fsaverage.inflated surface. From these  error messages I cannot really spot the issue- I guess it might be some kind of matrix dimension mismatch? Which confuses me, as I resampled the data to the fsaverage brain...?

I ran:

1. mris_preproc --fsgd 1234.fsgd --cache-in thickness.fwhm10.fsaverage

--target fsaverage --hemi lh --out lh.1234.10.mgh

2. mri_glmfit --y lh.1234.thickness.10.mgh --fsgd 1234.fsgd --C

1234.mtx --surf fsaverage lh --cortex --glmdir lh.1234.glmdir

--> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh

When I launch freeview and try to overlay sig.mgh manually, I get "Correlation data does not match with surface". Does this have something to do with the "apply registration option" and if so, what would I have to select here? (since the data should already be registered to fsaverage...?).

Thanks a lot,

Meike

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