Hi Doug, I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I also have a contrasts.sig.mgh file in the gmldir.
Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I retrieve this file? Thanks for your help! Clara ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 16. Februar 2017 19:22:01 Betreff: Re: [Freesurfer] cluster as ROI On 02/16/2017 04:24 AM, Clara Kühn wrote: > 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? input from preproc/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 there should be a bunch of output there from mri_glmfit and mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output may not be there. you'll have to run it separately. But there should be, eg, gamma.mgh there > > 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
