Re: [Freesurfer] cluster size threshold
You need to find the correct CDF file, eg, if the final FWHM is 12, it would be in $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th30/mc-z.cdf To get the FWHM look in glmdir/fwhm.dat and round down in the mc-z.cdf file, find the row where the MaxClustCDF drops below .05/2=.025, then look at the MaxClustBin for the critical cluster size On 2/24/2020 6:49 AM, Elisa Castaldi wrote: External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster _size_ threshold in this case? Where can I find this information? Thanks Elisa ___ 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
[Freesurfer] cluster size threshold
External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster *size* threshold in this case? Where can I find this information? Thanks Elisa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster size threshold for the sig.mgh file
Use the --minarea option doug Jürgen Hänggi wrote: Dear FS experts We would like to threshold the cluster size in the sig.mgh image in order to exclude clusters that are only a few vertices in size, but I cannot find this option Is it possible to do it within FS? If yes, how to do it? Thanks in advance Regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
