FreeSurfer MRI reconstruction Anatomical reconstruction The first processing stage is the creation of various surface reconstructions. Usually a full FreeSurfer reconstruction is obtained by the following commands: $ my_subject=sample $ my_NIfTI=/path/to/NIfTI.nii.gz $ recon-all -i $my_NIfTI -s $…

What is a NIFTI file and where to obtain it

jstout211 (Jeff Stout) November 24, 2023, 3:46pm 2

The nifti file is the T1 mri from your subject.

If you have dicoms - you can convert to nifti using dcm2nii (NITRC: MRIcron: Tool/Resource Filelist)

–Jeff

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