Hi experts,
I have three questions. I would really appreciate any help.
(1). I ran following commands to estimate relationships between LGI and Behav data:
mris_preproc --fsgd Behav.fsgd --target fsaverage --hemi lh --meas pial_lgi --out lh.Behav_LGI.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.Behav_LGI.mgh --fwhm 10 --cortex --tval lh.Behav_LGI.10.mgh
mri_glmfit --y lh.Behav_LGI.10.mgh --fsgd Behav.fsgd dods --C Corr-Behav-cor1.mtx --surf fsaverage lh --cortex --glmdir lh.Behav_LGI_P.glmdir --eres-save
mri_glmfit-sim_nonortho --glmdir lh.Behav_LGI_P.glmdir --sim perm 2000 1.3 permcsd --sim-sign pos --cwpvalthresh .05 --perm-resid --overwrite
Finally, cluster summary gives me one clusters with peak at the fusiform gyrus as following: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -4.045 10153 32101.81 -36.5 -39.5 -15.1 0.00050 0.00000 0.00100 64731 -106698.82 fusiform
As you can see number of voxels is 64731, so I when I viewed the results in FreeView, its showing me a big cluster, almost all over the brain (please see attached screen shot).
Could you please tell me why I am getting these sort of results, and how can I fix this? If I change cluster forming threshold from 1.3 to 3, would that work? I wanted to make sure before I re-run the analysis because mri_glmfit-sim_nonortho command takes about a day to finish.
(2). How can I save output cluster e.g. fusiform gyrus in above example in NIFTI MNI volume space so that I can use this cluster for functional connectivity analysis?
(3). If I want to use fusiform gyrus from standard FreeSurfer parcellation rather than from my results, how can I save that in standard MNI volume space?
Thank you so much !
