ps, you may want to smooth the wmh volumes, eg, mri_fwhm --smooth-only --i all.wmh.mgh --fwhm 5 --o all.wmh.sm05.mgh then use all.wmh.sm05.mgh as input to glmfit

On 04/08/2016 12:27 PM, Douglas N Greve wrote:

You can binarize each WMH volume, ie, mri_binarize --i aseg.mgz --match 77 --o wmh.mgz Convert to mni305 space with mri_convert wmh.mgz wmh.mni305.mgz --apply_transform transforms/talairach.xfm -oc 0 0 0

View to check (only need to do for one subject): tkmedit fsaverage orig.mgz -ov wmh.mni305.mgz

Concatenate all subjects together mri_concat subject1/mri/wmh.mgz subject2/mri/wmh.mgz ... --o all.wmh.mgz

After that you can do some simple statitics (eg, presence or abscence of WMH) mri_glmfit --i all.wmgh.mgz --no-prune --osgm --o glmfit

tkmedit fsaverage orig.mgz -of glmfit/osgm/sig.mgh

Not sure what you mean by subcortical surface

On 04/08/2016 08:07 AM, Dr Sampada Sinha wrote:

...

Dear freeesurfer experts,

I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR separately after processing T1 with recon-all. Presently, I don't have any dwi data where I can project the WMHs onto the WM tracts. Will you please tell me how do I project the WMHs of 29 MDD patients on a template (?) showing the WMH abnormalities? Or if you can please recommend a paper or freesurfer page from where I can get a step by step directions of showing WMHs of 29 cumulative MDD patients on subcortical surface.

Thanks and regards,

Sampada

-- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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