That will be the average value over the vertices in the ROI, which is not what you want for surface area. Add --accumulate to the mri_segstats command line to get the total area
On 02/21/2017 12:43 PM, Clara Kühn wrote: > I have one last question about the whole thing. > > What is the measurement in the output file? My subjects have values between > 0.6 and 1.5. As the measure is surface area I was expecting different > numbers. Do I have to multiply by some constant to get to mm²? > > Thank you > Clara > > ----- Ursprüngliche Mail ----- > Von: "ckuehn" <cku...@cbs.mpg.de> > An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Gesendet: Dienstag, 21. Februar 2017 18:28:25 > Betreff: Re: [Freesurfer] cluster as ROI > > ah! Perfect, thank you! I'll give that a try. > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 18:23:48 > Betreff: Re: [Freesurfer] cluster as ROI > > 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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