Hello,
I used recon-all -hippo subfields on an earlier version of free surfer (recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to view the subfields in freeview with versions earlier than 5.2. I noticed when I load all the subfields into free view and use the color LUT file, the subfields have pixelated colors at each voxel. Is there a way to view earlier versions of this similar to what is presented on the website (i.e., where subfields are represented by solid colors)? I assume this may be an issue with intensity values in the image?
Thanks, Danielle
Hi Danielle,
from the mri directory of a subject, run
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
and be a bit patient; it takes a little while to combine all the posteriors into the segmentation.
Cheers,
Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Danielle Miller" dmiller3@bu.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 27, 2015 4:40:57 PM Subject: [Freesurfer] hippocampal subfield viewing
Hello,
I used recon-all -hippo subfields on an earlier version of free surfer (recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website on how to view the subfields in freeview with versions earlier than 5.2. I noticed when I load all the subfields into free view and use the color LUT file, the subfields have pixelated colors at each voxel. Is there a way to view earlier versions of this similar to what is presented on the website (i.e., where subfields are represented by solid colors)? I assume this may be an issue with intensity values in the image?
Thanks, Danielle
freesurfer@nmr.mgh.harvard.edu
-
Danielle Miller -
Eugenio Iglesias