Hi Stephanos,

The easiest way is to extract label 206 (CA1) from [lr]h.hippoSfLabels-T1.v10.FSvoxelSpace.mgz using mri_extract.label, and then apply the resulting mask on the original (orig.mgz) or normalized (norm.mgz) volumes.

From the subject’s mri directory:

mri_extract_label lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 leftCA1.mgz mri_extract_label rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 rightCA1.mgz

mri_mask orig.mgz leftCA1.mgz orig_left_CA1.mgz mri_mask orig.mgz rightCA1.mgz orig_right_CA1.mgz

Then, you can do your analyses on orig_left_CA1.mgz and orig_right_CA1.mgz (you can for instance use the Matlab functions to do this)

I hope this helps

Cheers,

/Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 16 May 2017, at 20:08, Stephanos Leandrou <S.Leandrou@euc.ac.cymailto:S.Leandrou@euc.ac.cy> wrote:

Hello Freesurfer Developers,

I want to perform texture analysis on the CA1 subfield of the hippocampus. Thus, I am using the recon-all command to generate the subfields. However, I want to perform texture analysis on the CA1 subfield only and I need to extract it from the original T1 image… How can I do this, what are the steps to save the CA1 subfield only?

Thank you in advance…

Stephanos

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