I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues:
(1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps.
(2) A previous email suggested that there are stored values that I could lookup, but I can't seem to locate the files anywhere.
(3) With respect to the fwhm values used in the simulations, it was suggested that this be matched to the fwhm.dat file output from mri_glmfit; however, since I didn't use mri_glmfit, I don't have fwhm.data file. Should I just use the smoothing used on the surfaces?
Any thoughts would be appreciated.
Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
mri_mcsim just runs the monte carlo simulation that mri_glmfit runs (but more efficiently). Either way, you still need a FWHM to do a cluster-wise correction. You can probably run mri_glmfit (and mri_glmfit-sim) on the data that you use as input to your GLM software. Alternatively, you can have your software produce a file of residuals which you then run mris_fwhm to compute the FWHM. If you can't use the smoothing kernel size if you did volume smoothing. If you did surface smoothing, then the FWHM will be underestimated (I often find by a lot for functional data). doug
MCLAREN, Donald wrote:
I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues:
(1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps.
(2) A previous email suggested that there are stored values that I could lookup, but I can't seem to locate the files anywhere.
(3) With respect to the fwhm values used in the simulations, it was suggested that this be matched to the fwhm.dat file output from mri_glmfit; however, since I didn't use mri_glmfit, I don't have fwhm.data file. Should I just use the smoothing used on the surfaces?
Any thoughts would be appreciated.
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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MCLAREN, Donald