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 Cheers Clara ----- 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
