Hello Freesurfer Experts,

My apologies if this is a rather simple/obvious question. I am trying to run 3 Monte Carlos using mri_glmfit-sim with the following commands:

Left hemisphere surface: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../LH_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01

Right Hemisphere surface: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../RH_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01

Volume: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../MNI305_7vFix/ --sim mc-z 10000 1.3 mcz10000_1.3 --sim-sign abs -cwpvalthresh .01

I'm running this command after my mri_glmfit that includes the --no-prune flag (command below). While the Monte Carlos for the surface ran without problems, there is an error when I try to run the volume based analysis:

Error: could not determine file for /cluster/roffman/.../MNI305_7vFix//mask

I believe this error refers to the absence of a mask.mgh file. In my analysis the mask.mgh file is only generated for the fsaverage lh and rh surface analyses after mri_glmfit (when the --no-prune is included), while no mask file is generated for the volume. When I re-run the mri_glmfit command with --prune, the mask.mgh file is generated for the volume and the Monte Carlo appears to run. I don't know if this matters but we run our current volume analyses in the mni305 standard space (constructed via mkanalysis-sess with -mni305 2 and not the -native flag).

I'm a bit confused why a mask.mgh file isn't generated for the --no-prune volume analyses but is generated for the --no-prune surface analyses. If my mri_glmfit-sim error is referencing the lack of a mask.mgh file, is there a way that I could create a substitute mask.mgh file to feed into the Monte Carlo? Alternatively might there be another better way to work around the no mask error?

My mri_glmfit command for the volume is the following:

mri_glmfit --y $SUBJECTS_DIR/.../SIRP_Stable5.3_121316_sm5_mni305/7vFix/ces.nii.gz --fsgd /cluster/.../152_GDD_7vFix_Covary_Continuous_Serum_Folate_Linear_Nuis_GenderClass_Age_RT.fsgd --C /cluster/.../TwoGroups1CovariateRegressOut2covariates.mtx --glmdir /cluster/.../MNI305_7vFix/ --fwhm 6 --no-prune

I am running a Linux using Release 6.7 (Santiago) and Freesurfer 5.3 (nmr-stable53-env).

I would be most grateful for any suggestions or troubleshooting insights you might have!

Best wishes, Kevin

Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479