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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