I noticed that your DOF is 1290, so it is possible that you are maxing
out the float computation. By coincidence, I just reprogrammed this to
use double instead of float precision. You can get it from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit
username guest
pwd collab
Let me know if that fixes your problem
On 3/16/2023 9:47 AM, Yuri Yeshinsky wrote:
External Email - Use Caution
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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