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I have follow-up concerns. I also ran PALM as following to check my results: palm -i y.mgh -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh -d X.csv -t C1.csv -m mask.mgh -o plm -C 1.95996 -Cstat extent -twotail -n 5000 Interestingly, I get identical results (visually) between PALM (CFT = 0.05 i.e., 1.95996) and MCZ (CFT = 0.05 and CWT = 0.001). Outputs from both PALM and MCZ overlap (looks like almost completely). I have following few concerns (in addition to my previous questions from previous email): (1). Summary result file from MCZ gets automatically saved after running mri_glmfit-sim. And, to save summary result file from PALM I ran mri_binarize, mris_calc and mri_surfcluster commands (by looking at previous discussions in FreeSurfer forum). However, summary file from MCZ gives me two large clusters - with peaks within middle temporal and rostral middle frontal, whereas summary file from PALM gives me two large clusters of very similar size as of MCZ, but peaks within fusiform and lateral orbitofrontal. It seems that both MCZ and PALM give two clusters based on maxima using their other scheme - that's why although cluster sizes and overall maps are similar but peaks differ - causing different names in corresponding summary files despite the fact that I am using same annotation file for both. Below I am attaching both the summary results from PALM and MCZ. Could you help me in figuring out the way to generate correct and reportable summary file? If both are correct in their own way, I would really appreciate any explanation and preferable option here? (2). If both of the above options are correct and as I get consistent results from MCZ and PALM, then MCZ results clearly tell whether the correlation is negative or positive (by looking at the cache*.summary and cache*.cluster.mgh files. But I could not find a way from PALM results to make sure the correlation is negative or positive. All the outputs e.g., *.fwep.mgz and *.tstat.mgz show positive maps always. Could you help in finding the directionality of correlations from PALM option above? (3). Again, as my results are consistent between MCZ and PALM, and for MCZ I provide flag --2spaces (for Bonf. Correction of hemispheres) so I assume that the above PALM command does not perform Bonf Correction, so I applied Bonf Correction in mri_surfcluster command using the flag --bonferroni 2. Could you please confirm is that's the correct way? Thanks a lot for all your help. Following is the summary file from PALM: ….. ….. # SearchSpace_mm2 76467.1 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 1e-12 # Maximum Threshold 0.05 # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # Overall max 0.998 at vertex 66 # Overall min 0 at vertex 0 # NClusters 2 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs WghtVtx Annot 1 0.042 11 2023.40 -35.1 -23.3 -22.8 3523 147.97 fusiform 2 0.044 9 1923.92 -26.3 23.8 -6.0 3442 151.45 lateralorbitofrontal Following is the summary file from MCZ: ….. ….. # SearchSpace_mm2 76467.1 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.001 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1.1597 at vertex 125047 # Overall min -4.53083 at vertex 110270 # NClusters 2 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -3.405 136882 2024.82 -48.2 -1.6 -33.0 0.00020 0.00000 0.00040 3526 -6733.96 middletemporal 2 -4.531 110270 1924.64 -17.2 57.8 -13.3 0.00020 0.00000 0.00040 3444 -6888.13 rostralmiddlefrontal On Mon, Jan 6, 2020 at 2:58 PM Martin Juneja <mj70...@gmail.com> wrote: > Hi, > > I am using Monte-Carlo simulations (for cortical thickness and volume - > behavioral analysis) for clusterwise correction for multiple comparisons. > > My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e., > CWT = 0.07) (smoothing 12 mm) for cortical thickness-behavior analysis - > with maxima at -4.3 (CFT) > or (ii) CFT < 0.05 and CWT < 0.001 (i.e., CWT = 0.0002) (smoothing 10 mm) > for cortical volume-behavior - with maxima at -4.53 (CFT) > > Both the clusters in (i) (lateral orbital frontal) and (ii) (rostral > middle) are within the frontal cortex, but not overlapping ! > Also, although maxima is at (i) -4.3 and (ii) -4.53, still the clusters do > not survive recommended thresholds suggested in > https://www.ncbi.nlm.nih.gov/pubmed/29288131 > And the FPR in this paper at strong CWT (i..e, 0.001) and liberal CFT > (i..e, 0.05) is not calculated. > > So I was wondering if there is any recommendation from the experts > regarding these results, or none of these make sense because I never get > CFT < 0.001 and CWT < 0.05 (at-least). > > Any help would be really appreciated. >
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