Hi,

I am running a group analysis (patients versus controls). I am following the tutorial and managed to create the FSGD file with four classes

MSMale

MSFemale

HealthyMale

HealthyFemale

and one variable: Age

So the number of NregressorsDODS is equal to 8

[ MSMale MSFemale HealthyMale HealthyFemale Age_ MSMale Age_ MSFemale Age_ HealthyMale Age_ HealthyFemale ]

I have created my own contrast files as follows:

lh-female_MS_vs_Healthy

.mtx to
compare between Female MS and Female Healthy regardless of age
:

[ 0 1 0 -1 0 0 0 0 ]

lh-female_MS_vs_Healthy_Age
.mtx

to
compare between Female MS and Female Healthy_with age effect
:

[
0 0 0 0 0 1 0 -1
]

lh-male_MS_vs_Healthy
.mtx

to
compare between Male MS and Male Healthy regardless of age
:

[
1 0 -1 0 0 0 0 0
]

lh-male_MS_vs_Healthy_Age
.mtx to
compare between Male MS and Male Healthy_with age effect

:

[
0 0 0 0 1 0 -1 0
]

lh-MS_vs_Healthy
.mtx to compare between MS and Healthy regardless of Age and Gender
:

[
0.5 0.5 -0.5 -0.5 0 0 0 0 ] 

I ran the glm_fit using the following command line:

mri_glmfit --y lh.disease_Healthy_Age.thickness.10.mgh --fsgd disease_Healthy_Age.fsgd dods --C lh-MS_vs_Healthy.mtx --C lh-male_MS_vs_Healthy_Age.mtx --C lh-male_MS_vs_Healthy.mtx --C lh-female_MS_vs_Healthy_Age.mtx --C lh-female_MS_vs_Healthy.mtx --surf fsaverage lh --cortex --glmdir lh.disease_Healthy_Age.glmdir

Everything went OK except when loading the sig.mgh in freeview using the following command:

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh:overlay_threshold=4,5 -viewport 3d

1- It complained that the flag annot_outline=1 is not recognized
2- after removing this flag from the command line, t
he overlay only was two colors (green and red) (I have attached a copy of it)

Then I did
a cluster-wise correction for multiple comparisons

run

ing

a simulation
as follows:

mri_glmfit-sim --glmdir lh.disease_Healthy_Age.glmdir --cache 4 neg --cwp 0.05 --2spaces

Nothing has changed. in free view the same overlay.

I opened the "
cache.th40.neg.sig.cluster.summary

" file

and got the following:

# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

# CreationTime 2015/10/02-15:06:07-GMT

# cmdline mri_surfcluster --in lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/neg/th40/mc-z.csd --mask lh.disease_Healthy_Age.glmdir/mask.mgh --cwsig lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.mgh --vwsig lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.voxel.mgh --sum lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.cluster.summary --ocn lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.mgh --oannot lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white

# cwd /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU

# sysname Linux

# hostname ali-XPS-L501X

# machine x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

# Input lh.disease_Healthy_Age.glmdir/lh-MS_vs_Healthy/sig.mgh

# Frame Number 0

# srcsubj fsaverage

# hemi lh

# surface white

# annot aparc

# SUBJECTS_DIR /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/freesurfer_HU

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 149955

# Bonferroni 2

# Minimum Threshold 4

# Maximum Threshold infinity

# Threshold Sign neg

# 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 2.82441 at vertex 65720

# Overall min -3.14816 at vertex 26640

# NClusters 0

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 0

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

As you can see, the columns are empty!!!

Any ideas please? was there any mistake in my processing?

Many thanks for your help.

Ali

Ali M. Al-Radaideh. PhD

Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 3903333 ext.5422, 5355, 5364
Email: ali.radaideh@hu.edu.jo

webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=