What I have listed as fa.nii.gz should be the same file that you passed
to mri_glmfit with the --y option.
doug
Antonella Kis wrote:
> Dear Doug,
>
> THANKS SO MUCH for your help. My last questions is: I suppose the --i
> fa.nii.gz is an input file. What should be my input in thi scase if
> for
Oh, ok, I remember this now. Yes, you can use your mri_volcluster
command below the clusters. To get the table, run
mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz
--avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary
The fa.avg.dat will have a table of data. Each row will be
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 \
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
Dear Doug,
When I run the:
mri_glmfit-sim \
--glmdir GroupAnalysis_pos.glmdir \
--sim perm 1 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 G
