Hi Josh

the script recon-all will do everything you want. It is perfectly happy with nii files as input and will generate surfaces and segmentations including hippcampal labels. If you add one of:

recon-all --help | grep subfie -hippocampal-subfields-T1 : segmentation of hippocampal subfields using input T1 scan -hippocampal-subfields-T2 file ID : segmentation using an additional scan (given by file); -hippocampal-subfields-T1T2 file ID : segmentation using additional scan (given by file) and input T1 The following flags can be used to obtain a segmentation of the hippocampal subfields. -hippocampal-subfields-T1 -hippocampal-subfields-T2 file ID -hippocampal-subfields-T1T2 file ID

you will also get subfields. Running it is pretty simple (but slow, depending on your hardware):

recon-all \ -i <full path to input .nii file> \ -sd <dir to put each subject in> \ -s <unique identifier for this subject> \ -all

cheers Bruce

On Sun, 10 Apr 2016, Josh Rutta wrote:

Hi, I’m new to freesurfer, I’m an undergraduate currently doing research involving analyzing mri scans to produce volume measurements of the hippocampus. I’ve been using FSL’s FIRST method to do this thus far, but from what I’ve read online, freesurfer is much better for volumetric analysis of subcortical structures. The problem is that I can’t seem to find a good step by step tutorial to use free surfer. Also I’ve noticed free surfer runs on omgz files, and I’m dealing with nii files. I’d appreciate it if I could a step by step list of instructions on:

1. How to convert the nii files to mgz files correctly

2. getting volume of hippocampus from an mri scan

I appreciate the help, thanks!

Josh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer