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 mailto: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. i_n 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 <mailto:ali.radaideh@hu.edu.jo>
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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

_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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.

-- /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 mailto: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

What you use depends on what you are trying to do. Starting with the sig.mgh is good because it has not been corrected for multiple comparisons. You have a pretty high threshold (4, which means p<.0001). Try lowering it to 2 or even 1.3 to see if any activation pops out. At some point you'll need to correct for multiple comparisons.

On 10/2/15 1:51 PM, Ali Radaideh wrote:

Sorry, as I am quite new to this type of analysis, does the sig.mgh show any significance? if so how can I report it? I mean are they saved somewhere in SUBJECTS_DIR?

Also, it seems the corrected one does not show anything, am I true?

The last thing about this, shall I use sig.mgh or F.mgh?

Many thanks for your great help. Ali

On Fri, Oct 2, 2015 at 8:25 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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 <mailto: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. i_n 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 <mailto:ali.radaideh@hu.edu.jo>
    /
    /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto: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.




-- 
/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 <mailto:ali.radaideh@hu.edu.jo>
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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.

-- /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 mailto:ali.radaideh@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/

---

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