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 <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
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