I'm not sure what you mean/want. If you run preproc-sess with the -mni305 flag, it will resample to mni305 space and mask out non-subcortical structures

Normalize to mni

 

Dear Doug,

 

We have a very simple question. In a first step we segmented brains using the recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We would like to do some subcortical analysis and need to perfrorm this in MNI 305 space. We also need the subcortical labels for the actual analysis itself. Does someone know the trick? In short how do we get from fstcmc.nii.gz“ to subcortical functional ROI's?

 

Greetings Jan

Jan Willem Koten (van Grevenbicht)

Zollernstrasse 57, 52070 Aachen, Germany
Telephone: (0049) (0)241 212 44

 

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