Dear Doug, Unfortunately, it doesn't make a difference if I'm using a dot or comma or simply type in 2 or 3 as a threshold. The terminal output always shows me the converted version with a comma 2.3 --> 2,3 or 2 --> 2,0 which is not recognized by the command.
Maybe I have to change the default settings of floats in the bash using printf? Sincerely yours, Christopher -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Mittwoch, 10. Dezember 2014 17:31 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: > Dear Doug, > > I tried to run MCC with cluster-sess but unfortunately I got the same error > message like when I'm using mri_glmfit-sim. > It does not recognize the thresh (cluster-forming thresh) > > Here is the terminal output: > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/christopher/Desktop/freesurfer > FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects > MNI_DIR /home/christopher/Desktop/freesurfer/mni > FSL_DIR /usr/local/fsl > [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1 > [christopher@fu20a S1]$ cd $proj_dir > [christopher@fu20a S1]$ > [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis > DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos > ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > Sincerely yours, > > Christopher > > > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve > Gesendet: Montag, 24. November 2014 20:34 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] multiple comparisons correction for individual > hemispheres (native space) > > > Hi Christopher, sorry for the delay. I had a write a new program. You can > download it from here > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess > Let me know how it goes > > doug > > On 11/14/2014 06:05 AM, Milde, Christopher wrote: >> Dear Freesurfer experts, >> >> I performed fMRI analysis using FSFast resulting in uncorrected significance >> maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun >> selxavg3-sess with -fwhm at moment). >> >> How can I use simulations for native space hemispheres?. I tried to adapt >> mri_glmfit-sim but unfortunately it failed... >> >> Sincerely yours, >> >> Christopher >> >> _______________________________________________ >> 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. > > > _______________________________________________ > 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
