what about them?

On 10/2/15 1:20 PM, Ali Radaideh wrote:

Thanks Douglas,

The second line worked fine, but can I show you the results attached to this email?

Thanks,

Ali

On Fri, Oct 2, 2015 at 7:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

I notice from the image that the overlay is turned off. Try turning it on. Also, you can try

tksurferfv fsaverage lh inflated -aparc -ov sig.mgh

If that does not work, then

tksurfer fsaverage lh inflated -aparc -ov sig.mgh

On 10/2/15 12:08 PM, Ali Radaideh wrote:

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

​ by​

run

​ n​

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=

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--

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=

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.