Dear FreeSurfer experts, I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm with this: mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir
So far so good :) Now when I try to apply the Monte Carlo correction with this: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 --2spaces I get the error "fwhm: Undefined variable." So I tried to run the glmfit with the --y flag and use the lh.thickness_sm10.mgh file but I created that when registering and smoothing ALL my time points to the template, so I get this error: "ERROR: dimension mismatch between y and X. y has 224 inputs, X has 72 rows." I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm only an overwriting one. Should I register and smooth the data again for the separate time points or is there another way to deal with that? What could I do to correct my glm data? Cheers, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: [email protected] _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
