Hi Doug, I ran this command with the --no-y Flag: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y
and got the following error message: ERROR: Flag --no-y unrecognized. --glmdir /scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y Does the flag need to be at a certain position? Thanks for your help Clara ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:53:47 Betreff: Re: [Freesurfer] glmdir question By default it will compute a table. The rows of the table are each subject. The columns are the clusters. Each cell is the mean of the input for that subject over that cluster. It needs the input data to do this. On 05/26/2016 11:18 AM, Clara Kühn wrote: > I thought it had to be there because when I don't copy it into the glmdir I > get an error message that it can't find the mgh in said glmdir. > I'm gonna try running it with the flag you mentioned. > What does it mean, though, that it won't compute means over the clusters? > > ----- Ursprüngliche Mail ----- > Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Donnerstag, 26. Mai 2016 17:15:41 > Betreff: Re: [Freesurfer] glmdir question > > What is it doing in your glmdir? Usually you'd have it in another > location when running mri_glmfit (which creates the glmdir). In any > case, you can run it with --no-y and it will not look for the input file > (and will not compute means over the clusters). > > On 5/26/16 8:56 AM, Clara Kühn wrote: >> Dear FreeSurfer Experts, >> >> when running the Monte Carlo correction on a GLM I specify this command: >> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 >> --2spaces >> >> This assumes that my mgh file that I used as input for the GLM is in >> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM >> and create a new folder for this GLM I have to copy the mgh file into the >> glmdir to run the Monte Carlo correction. Is there a way to specify where >> that mgh is located so that I don't have a bunch of copies of it in all my >> glmdirs? >> >> Thanks for your help! >> Cheers >> Clara >> > _______________________________________________ > 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 > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
