---

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, December 5, 2011 11:53 AM
Subject: Re: [Freesurfer] DTI analysis and mri_glmfit-sim \

Hi Antonella, are there any clusters listed in the summary file? It might be that you just don't have any clusters that survive.
doug

Antonella Kis wrote:
> Dear all:
>
> I am doing an FA group study (controls vs. patients without any covariant so my C = +1.00000 -1.00000) and I want to see if there are any clusters that survives by multiple comparison so I ran:
>
> mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\
>      --fsgd DTI_group_analysis.fsgd --C contrast.mtx --glmdir group_analysis.glmdir
>
>
> and then:
>
>  mri_glmfit-sim \
>  --glmdir group_analysis.glmdir \
>  --grf 2 neg \
> --cwpvalthresh .025 \
>  --overwrite
>
> One of the output files is group_analysis.glmdir /contrast/sig.mgh which by my understanding is the significant uncorrected map which I can visualize it using freeview:
>
> freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
>            /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat
>
> The significant and corrected map containing the surviving clusters by multiple comparison should be the grf.th2.neg.sig.cluster.mgh  file but unfortunately when I try to visualize this clusters with Freeview I cannot see anything.
>
> Can you please give me an advise on how I can see this clusters over the group-fa-tal.nii?
>
> This is what I was trying and the only thing I can see is a white mask:
>
>
> freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
>            /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th2.neg.sig.cluster.mgh:colormap=heat
>
> Am I doing something wrong?
>
>
> Thank you for your time and help.
>
> Antonella
>
> ------------------------------------------------------------------------
>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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