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