Hi Doug,

I was trying to run what you suggested but seems that is still given me the error (without --seg):

ERROR: Input volume voxel dimensions do not match those 
in the registration file. If the input volume is in 
bshort/bfloat format, check that there is an accompanying 
bhdr file.


so I took out the --reg and it worked but I use the --seg from the cvs_avg35. Is correct to use this instead of the fsaverage (even if the register.dat from dt_recon is based
 on the fsaverage) or I should use fsaverage? In the wmparc2diff.mgz which I further use to create my fa-masks I used the register.dat files and I suppose they are coming from fsaverage but then I registered the FA data to
 CVS and I will need  to visualize the results on my CVS/mri/norm.mgz. Also is OK to eliminate the --reg option while running the mri_volcluster?



THANKS so much for helping, for making all this clear!
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 1, 2012 1:17 PM
 Subject: Re: [Freesurfer] Error with mri_glmfit-sim -- sim perm
  


It is looking for the aparc+aseg.mgz so it can report the segmentation that each cluster is in. If you don't need this information, then run this command:

mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05  --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh

I got this command out of your log file and removed the "--seg" part.

doug



Antonella Kis wrote:
> Dear all,
> 
> I was running the simulation:
> 
> 
 mri_glmfit-sim \
> --glmdir GroupAnalysis_abs.glmdir \
> --sim perm 1000 3 permcsd \
> --sim-sign abs \
> --cwpvalthresh .05
> 
> 
> and unfortunately I got the following error: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh
> 
> ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz
> 
> 
>
 Seems that the simulation was completed saying that mri_glmfit simulation done but I did not get any clusters or any file permcsd.sig.cluster.summary.
> 
> Also I am not sure if I need to use the while running the mri_volcluster the fsaverage or I should use the cvs_avg35  since my FA data was registered over the CVS space.
> 
> Can I just do something further to catch my corrected clusters? I attached my log file.
> 
> Thank you very much.
> 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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