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Dear FreeSurfer experts,

I ran many analyses on a large sample and everything goes well. However, I encounter here a problem I've never encountered before about one of my analyses. I'm looking at the presence of a difference in slope between three groups while covarying for several variables and classes. My contrasts are:

contrast1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0

contrast2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5

contrast3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5

6 classes (gender 2, disease 3), so first 6 for intercepts, next 30 for the covariates 1 to 5, and the last columns to test the slope difference between the three groups on the variable

I have used these contrasts to test the differences in slopes of several variables and I found significant clusters. However, for one variable specifically, mri_glmfit seems to be unable to quantify the FWHM from the data and when running mri_glmfit-sim, the resulting output, for every contrast (positive direction), gives a significant cluster where the whole cortex is included; see for contrast2 (it's the same result for every contrast anyways):

yuri@rodonor:/lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13$ cat cache.th40.pos.sig.cluster.summary

# Cluster Growing Summary (mri_surfcluster)

# 7.3.2

# 7.3.2

# CreationTime 2023/03/16-13:19:18-GMT

# cmdline mri_surfcluster --in lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh --mask lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh --cwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.mgh --sum lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.summary --ocn lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.masked.mgh --no-fixmni --csd-out lh.Cogn.moca.egfr.thickness.15.glmdir/csd/all.cache.th40.pos-Cogn-egfr-g13.csd --csd lab/yuri/FreeSurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm01/pos/th40/mc-z.csd --csdpdf lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.pdf.dat --vwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.mgh --vwsigmax lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.max.dat --oannot lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.annot --bonferroni 2 --surf white

# cwd /lab/yuri/egfrproject

# sysname  Linux

# hostname rodonor.bri.upall.sv

# machine  x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input      lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh

# Frame Number      0

# srcsubj fsaverage

# hemi lh

# surface white

# group_avg_surface_area 82220

# group_avg_vtxarea_loaded 1

# annot aparc

# SUBJECTS_DIR /lab/yuri/egfrproject

# SearchSpace_mm2 74258.8

# SearchSpace_vtx 144277

# Bonferroni 2

# Minimum Threshold 4

# Maximum Threshold infinity

# Threshold Sign    pos

# AdjustThreshWhenOneTail 1

# CW PValue Threshold: 0.05

# Area Threshold    0 mm^2

# CSD thresh  4.000000

# CSD nreps    10000

# CSD simtype  null-z

# CSD contrast NA

# CSD confint  90.000000

# Overall max 1e+10 at vertex 0

# Overall min 0 at vertex 8

# NClusters          1

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs    WghtVtx   Annot

   1     10000000000.0000       0  74258.42    -36.8  -18.3   64.5  0.00020  0.00000  0.00040  144276  1442760045363200.00  precentral

I feel that something is wrong in there, unless you think that it is possible that the slope difference manifests as a global effect for every contrast. It really seems to happen to happen specifically with this variable, as when replacing this variable by another, I can generate specific clusters that do not cover the whole cortex. Here is the terminal output from mri_glmfit when I run it on my "problematic" variable:

yuri@rodonor:/lab/yuri/egfrproject$ mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir

gdfRead(): reading analysis/egfr-Cogn-moca-egfr.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 60.1017 7.57085

1 Bmi 26.8664 4.97535

2 FRS 10.9088 9.29652

3 wm 1642.17 1761.49

4 educ 3.48198 0.959607

5 moca 27.2733 2.25488

Class Size and Means of each Continuous Variable

1 g1gender0 324  57.7939  25.8998   5.0538 1164.8920   3.4753  27.6883

2 g1gender1 309  58.2326  27.0854  14.3098 1722.7615   3.4822  26.9450

3 g2gender0 311  61.0777  26.8550   6.1809 1492.9781   3.4084  27.6785

4 g2gender1 345  62.4106  27.2979  16.8165 2059.6704   3.5391  26.8986

5 g3gender0 20  63.1610  27.9590   6.8020 1252.0200   3.4500  27.4000

6 g3gender1 23  67.2335  30.2713  26.5796 3377.0609   3.7391  25.8696

INFO: gd2mtx_method is dods

Reading source surface /lab/yuri/FreeSurfer/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces    327680

Total area         65417.000000

AvgVtxArea       0.399269

AvgVtxDist       0.721953

StdVtxDist       0.195472

7.3.2

cwd /lab/yuri/egfrproject

cmdline mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir

sysname  Linux

hostname rodonor.bri.upall.sv

machine  x86_64

user     yuri

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh

logyflag 0

usedti  0

FSGD analysis/egfr-Cogn-moca-egfr.fsgd

labelmask  /lab/yuri/FreeSurfer/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.Cogn.moca.egfr.thickness.15.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.Cogn.moca.egfr.thickness.15.glmdir

Loading y from /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh

   ... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.Cogn.moca.egfr.thickness.15.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 6285.08

Matrix condition is 8.72285e+09

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 144277 voxels in mask

Saving mask to lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 71879.345725

DOF = 1290

Starting fit and test

Fit completed in 28.4991 minutes

Computing spatial AR1 on surface

WARNING: ar1 = 0 <= 0. Setting fwhm to 0.

Residual: ar1mn=0.000000, ar1std=0.000000, gstd=0.000000, fwhm=0.000000

Writing results

  Cogn-egfr-g12

    maxvox sig=1e+10  F=0  at  index 0 0 0    seed=1679933797

Computing efficiency

  Cogn-egfr-g13

    maxvox sig=1e+10  F=0  at  index 0 0 0    seed=1679933797

Computing efficiency

  Cogn-egfr-g23

    maxvox sig=1e+10  F=0  at  index 0 0 0    seed=1679933797

Computing efficiency

mri_glmfit done

Many thanks,

Yuri

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