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> 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> 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
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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
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.