Hi Doug,

thanks for your input. Could you specify some of the flags for me? 

--i tp1.stack.mgh - is this supposed to be the cluster or file in my 
/template/surf/ folder that I get from mris_preproc and mris_surf2surf? 
--seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. The 
only files I have in the contrast folder are 2 .mat files


----- Ursprüngliche Mail -----
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 15. Februar 2017 23:35:54
Betreff: Re: [Freesurfer] cluster as ROI

Use something like this

mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh 
--excludeid 0 --avgwf tp1.clustermean.dat

The output tp1.clustermean.dat will be a matrix with nsubjects rows and 
nclusters columns where the value represents the mean for that subject 
in that cluster.

On 02/14/2017 11:47 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
> that survives Monte Carlo correction. Now I would like to extract the data 
> for each participant and each time point from that cluster so that I can plot 
> the change.
> How could I do this? I tried this so far:
> aparcstats2table --qdec-long $SUBJECTS 
> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
> --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
> But I get this error:
> ERROR: The stats file 
> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>  is not found or is too small to be a valid statsfile
> Use --skip flag to automatically skip bad stats files
> Do I have to define my cluster as a ROI and then warp it onto the single time 
> points? How would I do that?
> Any help is much appreciated!
> Thank you
> Clara

Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422

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