The fwhm.dat file contains the total amount of smoothness. The data have inherent/endogenous smoothing and then you apply a certain amount, so the total amount is different (more than) the amount you applied. To do correction for multiple comparisons, mri_glmfit-sim needs to know how smooth your data are (it needs the total smoothness). Smoothing by 25mm is a lot I think. I usually use 5-10mm.
On 6/29/17 9:50 AM, Van Der Deijl, Rosanne wrote:
Hi,
I have a question about mri_glmfit. As an input, you give e.g. the stacked thickness data from all subjects, smoothed with a certain fwhm. But then as an output file, it gives an fwhm.dat file, which, at least in my case, contains another smoothing level.
I noticed this because I ran mri_glmfit-sim forclusterwise multiple comparison correction, which gives me the error:
ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/rh/cortex/fwhm33/abs/th13/mc-z.csd
As input I gave data smoothed to 25fwhm, and not fwhm33, as it seems to think. But indeed, in the fwhm.dat file it gives fwhm = 32.940499.
I read in the tutorial that the fwhm.dat file contains the average FWHM of the residual. But still my questions are:
- what this means
- why mri_glmfit-sim would need this number, and whether/how I can run
the mult. comparison correction on the 25fwhm-smoothed data.
Thank you in advance!
- Rose
Commands: mri_glmfit: mri_glmfit --fsgd $CALMGREY/CALM_FSGD.txt dods --C CALMlong_contrast1.mat --C CALMlong_contrast2.mat --C CALMlong_contrast3.mat --C CALMlong_contrast4.mat --glmdir rh.CALMlong.thickness-spc.fwhm25 --y rh.CALMlong.thickness-spc.stack.fwhm25.mgh --cortex --surf fsaverage rh
mri_glmfit-sim: mri_glmfit-sim --glmdir rh.CALMlong.thickness-spc.fwhm0 --cache 1.3 neg --cwp --2spaces
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