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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