I'm pretty sure this is due to the language locale settings. Can you do an experiment? Run
echo $LANG if the result is not en_US.utf8 try setenv LANG en_US.utf8 And see if that fixes it. If it does, I can change the script doug On 12/11/2014 03:11 AM, Milde, Christopher wrote: > Dear Doug, > > Unfortunately, it doesn't make a difference if I'm using a dot or comma or > simply type in 2 or 3 as a threshold. The terminal output always shows me the > converted version with a comma 2.3 --> 2,3 or 2 --> 2,0 which is not > recognized by the command. > > Maybe I have to change the default settings of floats in the bash using > printf? > > Sincerely yours, > > Christopher > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve > Gesendet: Mittwoch, 10. Dezember 2014 17:31 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] multiple comparisons correction for individual > hemispheres (native space) > > > Are you using 1.3 or 1,3 ? > > On 12/09/2014 03:10 AM, Milde, Christopher wrote: >> Dear Doug, >> >> I tried to run MCC with cluster-sess but unfortunately I got the same error >> message like when I'm using mri_glmfit-sim. >> It does not recognize the thresh (cluster-forming thresh) >> >> Here is the terminal output: >> >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /home/christopher/Desktop/freesurfer >> FSFAST_HOME /home/christopher/Desktop/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /home/christopher/Desktop/freesurfer/subjects >> MNI_DIR /home/christopher/Desktop/freesurfer/mni >> FSL_DIR /usr/local/fsl >> [christopher@fu20a S1]$ 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
