Hi Viola, I have a different work flow for you. When you run FDR, it will change the "Min" value under "Threshold". Go to a terminal and cd to the contrast directory of your qdec output folder, then run the commands below. It is assumed below that the threshold you want to use is 3.37. You should replace that with the threshold found by FDR. The files with the "337" can be named anything. I just put "337" to make them unique.
doug
cd QDECOUTPUTDIR/CONTRAST mri_surfcluster --in sig.mgh --thmin 3.37 --subject fsaverage --hemi lh \ --sum cluster.337.summary.dat --ocn cluster.337.seg.mgh \ --annot aparc --oannot ./cluster.337.seg.annot
mri_segstats --seg cluster.337.seg.mgh --excludeid 0 --i ../y.mgh \ --sumwf cluster.337.wf.dat
cluster.337.wf.dat will be a text table with number of rows equal to the number of subjects and number of columns equal to the number of clusters. To see which cluster is which, run
tksurfer fsaverage lh inflated -annot ./cluster.337.seg.annot -curv -gray
Each cluster will have a color and a number.
On 07/24/2012 02:52 AM, Oertel, Viola wrote:
Okay. And how I do the clusterwise correction? In which window does it appear?
Viola
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von"Douglas Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 24. Juli 2012 04:06 Bis: Oertel, Viola; free surfer Betreff: Re: [Freesurfer] stats
Neither of these tables is the one you want. Those are tables of standard freesurfer ROIs and are unrelated to your map-based analysis. You will need to do the cluster-wise correction for multiple comparisons using the voxel-wise threshold that FDR found. Set the cwp (cluster-wise p-value) threshold to 1 so that you get all of the clusters. When you do the clusterwise correction, it will produce a file with the values you want. doug
On 7/23/12 2:44 AM, Oertel, Viola wrote:
Hi Doug, I did the correction for multiple comparisons (FDR 0,05). Then, I have seen significant clusters in the map. After that, I run the generate tables stat (or so on) button and got two tables with thickness values. But I don't know which one of the tables is the right one because this step produced two files:
lh.aparc.a2005s.thickness.stats and lh.aparc.thickness.stats
May you tell me which one is the right, and are these results only the significant areas, or all computed once?
Thanks, Viola
Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Freitag, 20. Juli 2012 21:26 Bis: Oertel, Viola; Freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] stats
Hi Viola, those stats tables are unrelated to your map-based exploratory analysis. If you have clusters in your map, you should run the correction for multiple comparisons. This will give you significant clusters. It will also produce a table of mean thicknesses in each cluster for each subject which you can then import to SPSS. doug
On 07/19/2012 04:35 PM, Oertel, Viola wrote:
Yes. I did the contrast pat. vs. cont and see some significant regions on the display. After that, I did this "generate" stats table. My idea was to put this scores into SPSS and run the inferential statistics there. But I am not sure which table I have to use. What I want to use are the thickness values of each participant of all significant regions which I can see on the template. Currently, I am not sure what kind of regions the tables show? Are that all regions, only the significant ones of the specific contrast I compute? I have seen that both tables show different regions. But I currently don't how the selection works.
May you help with that?
Thanks and best regards,
Viola
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von"Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 19. Juli 2012 17:30 Bis: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] stats
Those stats tables just gives statistics (means, standard deviations) for thickness in different regions. They do not have inferential statistics. Have you run an analysis on patients vs controls? doug
On 07/19/2012 09:27 AM, Oertel, Viola wrote:
Dear Doug,
I have a question: when I create the stats tables, there are two tables:
lh.aparc.a2005s.thickness.stats and
lh.aparc.thickness.stats
which one is the right one if I want to get the thickness values of the significant clusters from the main effect (pat. / controls)?
Thanks and best regards,
Viola
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