Hm. It either doesn't recognize the --no-y flag (no matter at which position) or it doesn't recognize the --mczsim flag.
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 18:58:39 Betreff: Re: [Freesurfer] glmdir question Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim On 05/26/2016 12:53 PM, Clara Kühn wrote: > 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
