*By default, FreeSurfer compputes and uses a two-tailed p-value. When you specify a sign, it lowers the threshold that you give it to reflect a one-tailed test. Probably what happened was that you had two clusters close to each other that merged together with the lower threshold. doug * Antonella Kis wrote:
Dear Doug,
Finally I've got it. But there is one more problem: when I run the QDEC with Min threshold 2 neg, I am getting 2 clusters, while when I am running the results from QDEC(under Untitled.glmdir) with the -sim:
mri_glmfit-sim \ --glmdir Untitled.glmdir \ --cache 2 pos \ --overwrite
I am getting only one of the clusters. Can you please advise me what is going on or what should I correct?
Many thanks, AK
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, September 28, 2011 1:33 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim
again, FDR should have nothing to do with it. If you want a voxel-wise threshold at 2, just set that threshold when you run mri_glmfit-sim with "--cache 2 sign" where sign is pos, neg, or abs doug
Antonella Kis wrote:
Hi Doug,
Thanks again for helping. I am trying to use QDEC but there are no
clusters surviving after FDR (it says statics cannot be done so gives me error by running FDR). So I am trying to get the thickness values only for the clusters that are formed in QDEC after setting up a threshold = 2 (before running FDR). In order to do this you suggested me to run mri_glmfit-sim on the QDEC results. The only problem is that 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
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com> *Cc:* "freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Wednesday, September 28, 2011 12:06 PM *Subject:* Re: [Freesurfer] Error with mri_glmfit-sim
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_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison?
Many thanks, AK
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve