Re: [Freesurfer] Qdec plot design

FDR does not have blobs either, but I think I get what you mean:). You should run mri_surfcluster specifying the FDR-determined voxel-wise threshold as the --thmin, the sig.mgh as the --in, --subject fsaverage --hemi the-hemi-you-use, and --ocn ocn.mgh

Then

mri_segstats --i y.mgh --seg ocn.mgh --excludeid 0 --avgwf y.ocn.dat --sum ocn.sum

Where y.mgh is the input stack used for glm analysis. The y.ocn.dat will have number of rows equal to the number of subjects and number of columns equal to the number of clusters

On 11/07/2016 04:49 PM, Mihaela Stefan wrote:

I'm sorry, I might not have used the right word. Let's say 'blob' instead of cluster. It's something like the plot attached. Each circle/square is a subject. I would like to export that so I can make the plot myself. Best, Mihaela

On Mon, Nov 7, 2016 at 4:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

What do you mean a "plot"? I had assumed you wanted to average over
clusters, but FDR does not produce clusters


On 11/07/2016 04:26 PM, Mihaela Stefan wrote:
> That seems to be for Monte Carlo simulation. What if I use FDR
or if I
> want to look at a plot from an uncorrected map?
>
> Thanks!
> Mihaela
>
> On Mon, Nov 7, 2016 at 3:16 PM, 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>>> wrote:
>
>     Run mri_glmfit-sim using the Qdec output folder as the
--glmdir and
>     setting the thresholds and signs as you had them in qdec.
The output
>     will then be in a file called something like
cache.th20.pos.y.ocn.dat.
>     the cluster summary table will be in
>     cache.th20.pos.sig.cluster.summary
>
>
>     On 11/07/2016 12:33 PM, Mihaela Stefan wrote:
>     > Hello Freesurfers,
>     >
>     > I am doing a group analysis using Qdec. I have a few
significant
>     > clusters and I would like to plot one of them. Qdec does
that if I
>     > click on 'Find Clusters and Goto Max' but I don't see options
>     for the
>     > design of the plot.
>     > How can I export the thickness values from my cluster to
>     reproduce the
>     > Qdec plot in another program?
>     >
>     > Thank you!
>     > Mihaela
>     >
>     >
>     > _______________________________________________
>     > 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
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>
>     --
>     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 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
>     Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
>
>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
>     <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
>     Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>     <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
>
>     _______________________________________________
>     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
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>   
 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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
<http://www.partners.org/complianceline>
>     <http://www.partners.org/complianceline
<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.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer