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
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.glm
Hi,
I was trying to run for my FA group study the following:
mri_glmfit-sim \
--glmdir Group_Analysis.glmdir \
--sim neg perm 1 3 permcsd\
--cwpvalthresh .05
but I got an error: Flag permcsd unrecognized and then is asking me agout --sim
sign.
Can you please help?
THANK YOU!
Antonella
__
Is this volume data? If so, then use --grf with mri_glmfit-sim instead
of --cache.
doug
Antonella Kis wrote:
> Dear Doug,
>
> Can you please advise me how I can do a multiple comparison for my DTI
> group analysis?
>
> I tried and I ran:
>
> mri_glmfit --y group-fa-tal.nii
> --fsgd DTI_group
>>> I cannot run the -sim if there is no FDR data (stats) so I cannot
>>> cache the clusters formed only by thresh 2 in QDEC. Is theer a way to
>>> do it?
>>>
>>> Many thanks,
>>> AK
>>>
>>> ------------
>>> *Fro
a way to
> do it?
>
> Many thanks,
> AK
>
>
> *From:* Douglas N Greve
> *To:* Antonella Kis
> *Cc:* "freesurfer@nmr.mgh.harvard.edu"
> *Sent:* Wednesday, September 28, 2011 12:06 PM
> *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim
Good afternoon,
I tried running the -sim on my QDEC output (as recommended last days) but for
some data the FDR gives me error (cannot calculate clusters statistics) so
mri_glmfit-sim is not working either since the corrections by multiple
comparisons is not working. What should I do in t
What does FDR have to do with it? FDR should not come into play in this.
doug
Antonella Kis wrote:
> Good morning Doug,
>
> I tried running the -sim on my QDEC output (as you recommended me last
> days) but for some data the FDR gives me error (cannot calculate
> clusters statistics) so mri_glmf
Good morning Doug,
I tried running the -sim on my QDEC output (as you recommended me last days)
but for some data the FDR gives me error (cannot calculate clusters statistics)
so mri_glmfit-sim is not working either since the corrections by multiple
comparisons is not working. What should I do
