Hi Doug,

Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option?
Also, when I am visualizing my clusters using tkmedit:

tkmedit cvs_avg35 norm.mgz \
  -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \
  -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh  \
       /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \
  -fthresh 0.2 -fmax 1

I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)?

How can I get my FA values within each cluster in a table?



Thank you so much.
Antonella


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: Wednesday, February 8, 2012 11:37 AM
Subject: Re: Reposting: Clusters by Multiple comparison

Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log.  If you need to run it for debugging purposes, you can run it with 10 iterations  (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why.
doug

Antonella Kis wrote:
>
>
> Dear Doug,
>
> When I run the:
> mri_glmfit-sim \
> --glmdir GroupAnalysis_pos.glmdir \
> --sim perm 10000 3 permcsd \
> --sim-sign pos \
> --cwpvalthresh .05
>
> I am not getting my clusters file permcsd.sig.cluster.mgh  with the clusters summary so as you recommended I am running the
>
> mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh
>
>
> My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an  fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space?
>
> Thank you.
> AK
>
>

-- 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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