Oh, sorry, I precompute the tables with certain fixed voxel-wise thresholds. But it seems like you may want to use 2.3. Why 1.7? If you want it to match what you see in QDEC at a threshold of 2.0, then you should spec 2.3.
Antonella Kis wrote:
I am not sure but I tried that and it gives me error:
? --glmdir Untitled.glmdir \ ? --cache 1.7 neg\ ? --overwrite ERROR: thresh = 1.7, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 So how should I fix that?
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 4:07 PM *Subject:* Re: [Freesurfer] THANKS
The change in threshold is always 0.3. Eg, to go from a two-tailed threshold of 2.0 to a one-tailed threshold, you would subtract .3 from 2.0 (and so 1.7). Is this what you mean?
Antonella Kis wrote:
I see. Is there a way that I can get/read both clusters sin other
words can I eliminate this inconvenient of two-tailed p-value?
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>;
freesurfer <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Wednesday, September 28, 2011 2:59 PM *Subject:* Re: [Freesurfer] THANKS
*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
mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com
<mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>; freesurfer
<freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto: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 <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>>
*To:* Antonella Kis <atorok9@yahoo.com
mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>>
*Cc:* "freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>>"
<freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <mailto: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
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<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
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-- 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
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-
Douglas N Greve