External Email - Use Caution Hi Freesurfer Developers,
I'm conducting along-tract statistics using trac-all -stat and mri_glmfit-sim in FS v7.3.2, and I'm hoping to produce coordinates of where significant clusters are located along the mean tracts in template space. I've attached an example of my cluster summary txt files and have two questions: 1) Is it expected that this analysis would produce voxel indices for the output file (e.g., VoxX) rather than coordinates? 2) If so, what might be the best way to report coordinates in template space? I've overlaid the statistical outputs on the template tracts for visualization in freeview as described at the end of the Tracula tutorial ( https://secure-web.cisco.com/168WgBh44N5UFj4ozgWFlHSW0vhEupgM52Ka0yY-taK9tNmfBc1KmKjFIMrKXIUPG3jtAGvWih0Ir9Y8e_GwME9LFYFDbZnTjZUG0DxfealmcwuuxgROv-j0PZJW3tiTyOhl94Dp08L5tkYOPdn8uIoM-CO8ddvxGmixFuaOuN4-hIJ_EUoG_NKlgyx6bSQZlaC2FLPRO4f-aktWQ6QXVnCOi9uI1ajHCzym4tCtof0V45cxgoNHQeSsfZMuVfs6hvd85JLQ25E2DcYhzC4kdBtc652lUEznT02isAjVyjkCzFMj_9amQDnpT2H6q7FowagjTjIld5YwlqylmsvYfwQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics%23Visualizingresultsfromstatisticalanalysesalongapathway), but I'm wondering if there is a more efficient and exact way to determine coordinates of these clusters along the template tracts. Thank you for any clarification you can provide. Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin
# Cluster Growing Summary (mri_volcluster) # 7.3.2 # cwd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/t1prep # cmdline mri_volcluster --in /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/sig.mgh --mask /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/mask.mgh --no-fixmni --cwsig /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.cluster.mgh --sum /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.cluster.summary --ocn /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.ocn.mgh --cwpvalthresh .05 --out /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.masked.mgh --allowdiag --maxcwpval /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.max.cwpval.txt --gte --csdpdf /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.pdf.dat --csd /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/csd/perm.th13.abs.j001-matrix_tbi.txt.csd --vwsig /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.voxel.mgh --vwsigmax /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/perm.th13.abs.sig.voxel.max.dat # sysname Darwin # hostname PSYC-A30765 # machine x86_64 # user mbm3668 # Input Volume: /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/matrix_tbi.txt/sig.mgh # Frame Number: 0 # VoxSize_mm3 3.375 # SearchSpace_mm3 239.625 # SearchSpace_vox 71 # Minimum Threshold: 1.3 # Bonferroni 0 # Maximum Threshold: inifinity # Threshold Sign: abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 3.375 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: /Volumes/schnyer/Makenna/DODADNI/BIDS/derivatives/tracula/stats_outputs/tbi/rh.cst.FA_max.glmdir/mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 1 # NClusters 1 # CSD thresh 1.300000 # CSD nreps 1000 # CSD simtype perm # CSD contrast matrix_tbi.txt # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max CWP CWPLow CWPHi 1 5 16.9 67.00 0.00 0.00 -2.56128 0.03896 0.03100 0.04700
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