sorry, gave you the wrong flag. Use --sumwf instead of --accumulate
On 02/21/2017 01:08 PM, Clara Kühn wrote: > that doesn't change the values. I've attached the file for you. > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 18:56:17 > Betreff: Re: [Freesurfer] cluster as ROI > > 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 > > > _______________________________________________ > 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. 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.
