Re: [Freesurfer] Cortical thickness_Group analysis

Hi Ali, the FSGD and contrast matrices look right as do your command lines. What is the problem?

On 6/8/17 1:40 PM, Ali Radaideh wrote:

Dear Douglas,

Can I check with you if you have received my reply below to your question??

Thanks, Ali

On Mon, Jun 5, 2017 at 10:16 PM Ali Radaideh <ali.radaideh@hu.edu.jo mailto:ali.radaideh@hu.edu.jo> wrote:

Thanks alot.

Below are the commands I used in order:

mris_preproc --fsgd disease_Healthy_Age.fsgd --target fsaverage
--hemi lh --meas thickness --out
lh.disease_Healthy_Age.thickness.00.mgh

mri_surf2surf --hemi lh --s fsaverage --sval
lh.disease_Healthy_Age.thickness.00.mgh --fwhm 10 --cortex --tval
lh.disease_Healthy_Age.thickness.10.mgh


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


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

On Mon, Jun 5, 2017 at 4:03 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    what is your mri_glmfit command?


    On 6/4/17 8:10 PM, Ali Radaideh wrote:

...

    Dear FS experts,

    I am trying to analyse the cortical thickness for a group of
    MS patients and healthy controls. I have followed the
    instructions on how to perform group analysis but I am still
    unable to achieve what I am looking for.

    I am trying to produce a significance map to show the
    cortical areas that are statistically different between MS
    and healthy controls (in terms of cortical thickness).

    Would it be possible please to show you the matrix (fsgd) and
    contrasts files that I have used in my analysis?

    Best regards and many thanks in advance,

    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=/



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

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