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/
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
_______________________________________________
Freesurfer
mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The
information in this e-mail is intended only for the person to whom it is
addressed.
If you believe this e-mail was sent to you in error and the e-mail
contains
patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline .
If the e-mail was sent to you in error
but
does not contain patient information, please contact the sender and properly
dispose
of the e-mail.