Hi Carl, this is hard to say in advance. Do you see the internal band (the "swiss roll" or "dark band") of the hippocampus in your scans? If so, then I would go for it. If not, I would trade a bit of slice separation for in-plane resolution. If you want, feel free to send me a capture of a representative coronal slice in the hippocampal body. 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 ----- Original Message ----- From: "Carl Pintzka" <carl.pint...@ntnu.no> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, September 17, 2015 2:50:23 PM Subject: [Freesurfer] Scanner parameters for hippocampal subfield segmentation in Freesurfer 6.0 Hi, We are currently planning a population based MRI study and are interested in including a T2w scan that allows us to perform the new automatic hippocampal subfield segmentation included in Freesurfer 6.0. The current scanner settings (which has been used in a previous study) are as follows: 3T Siemens Skyra T2w turbo spin echo TR: 67 60, TE: 84 In plane resolution: 0.57x0.57mm Slice thickness: 1mm, no gap NAX: 3 In the Iglesias 2015 paper, 0.4x0.4 in plane resolution with 2mm slice thickness is used. Is this preferable since we intend on using the subfield segmentation on our dataset, or is it ok with 0.57x0.57 in plane resolution and thinner slices? We are not planning on performing manual segmentation on the dataset and thus want the settings to be optimal for the Freesurfer segmentation. What about number of averages? Best regards, Carl Pintzka _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
