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:
External Email - Use Caution
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:
- mris_preproc --fsgd 1234.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi lh --out lh.1234.10.mgh
- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer