then that is the "ocn" file to use with mri_segstats
On 02/21/2017 12:18 PM, Clara Kühn wrote: > yes! > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:58:37 > Betreff: Re: [Freesurfer] cluster as ROI > > Does this file exist? > > /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.ocn.mgh > > > On 02/21/2017 11:54 AM, Clara Kühn wrote: >> I've attached it for you as a .txt file >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> An: freesurfer@nmr.mgh.harvard.edu >> Gesendet: Dienstag, 21. Februar 2017 17:47:23 >> Betreff: Re: [Freesurfer] cluster as ROI >> >> Can you send the terminal output? >> >> >> On 02/21/2017 11:44 AM, Clara Kühn wrote: >>> Hm. I already did that. In none of my glmdirs are files like the >>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran: >>> >>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir >>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces >>> >>> Cheers Clara >>> >>> ----- Ursprüngliche Mail ----- >>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >>> An: freesurfer@nmr.mgh.harvard.edu >>> Gesendet: Dienstag, 21. Februar 2017 17:24:02 >>> Betreff: Re: [Freesurfer] cluster as ROI >>> >>> You will have to run mri_glmfit-sim >>> >>> >>> On 02/21/2017 04:07 AM, Clara Kühn wrote: >>>> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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. 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