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Yes, this is the expected behavior, ie, it should cover only subcortical GM regions. It is expected that cortical regions will be handled with the surface based analysis. You can recombine the results at the end with vlrmerge.

On 4/26/2023 12:22 PM, Elmira Hassanzadeh wrote:

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Hi everyone,

We preprocessed resting-state data with preproc-sess. In the output, I noticed although fmcpr.nii covers the whole brain, fmcpr.sm6.mni305.2mm.nii is only covering brain stem+cerebellum (screenshots attached).

Any clue what went wrong? This is an example of the command we ran for one of our subjects(R19):

preproc-sess -surface R19 lhrh -s R19 -fwhm 6 -fsd rest -mni305 -per-run

Thanks,

Elmira
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