What is a NIFTI file and where to obtain it

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1

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 $my_subject -all

In $ my_NIfTI=/path/to/NIfTI.nii.gz, what is the data of “NIfTI.nii.gz” and where can it be downloaded and run offline?

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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