Hi Freesurfer Team, We would like to compare Z-scored surface maps between different modalities (MRI and PET) within a single group. 1 subject = 2 measures.
These are my steps so far, using mri_concat and fscalc for the generation of the Z score maps. Differences between Z-score maps are tested using the paired t-test approach as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis I am not sure if my following steps are correct, so confirmation will be much appreciated, many thanks for your time and help! // Generate mean/sd of healthy controls X mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh --mean mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh --std Y mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh --mean mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh --std QN: Should smoothing be applied here or before? // Derive individual Z-score map for X and Y X for i in `cat list`; do fscalc $i/surf/lh.X.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o $i/surf/lh.Z.thickness.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.X.fsaverage.mgh sub group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o $i/surf/rh.Z.thickness.fsaverage.mgh; done Y for i in `cat list`; do fscalc $i/surf/lh.Y.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o $i/surf/lh.Z.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.Y.fsaverage.mgh sub group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o $i/surf/rh.Z.fsaverage.mgh; done // Derive paired-difference of Z scores between X and Y mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh // Smooth concatenated maps of paired differences mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval concat_XminusY_lh.mgh --tval concat_XminusY_lh_sm4.mgh // Test significance of paired differences within the group mri_glmfit --y concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods --osgm --surf fsaverage lh --cortex --glmdir I used the --osgm flag as there are no covariates here.
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