Libby,

Use mri_glmfit-sim instead of mri_glmfit. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

If you use just mri_glmfit then you have to use mris_surfcluster to get CWP information from .csd file.

pratap

hello,

i am working through the group analysis and multiple comparisons corrections tutorial using my own data. according to the tutorial, after running this command:

mri_glmfit --y lh.thickness.10.mgz --glmdir LH_MRT_agecovar.glmdir -- fsgd matrixT_FSGD --surf fsaverage lh --fwhm 10 --C MRT_agecovar.mtz -- sim mc-z 100 1.3 mc-z.negative --sim-sign neg

i should find CSD files in the LH_MRT_agecovar.glmdir/csd directory. my problem is that there is no /csd directory made as a result of the command that i run. there are also no CSD files in the contrast subdirectory. there is one CSD file (located at the same level as my glmdir) called:

mc-z.negative-MRT_agecovar.mtz.csd

but this file does not contain any CWP information.

i'm running version 4.1.0 on fedora 10

any help would be much appreciated.

thanks! libby

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer