Dear FreeSurfer experts,
We want to implement a deface method to ensure anonymity of participants before making the data available to researchers. Because the raw data is stored on the imaging platform XNAT, we preferred the mask_face method implemented on the XNAT server rather than FreeSurfer’s defacing. However, we will be using FreeSurfer for processing and segmentations afterwards. I am currently investigating the effect of face and earmasks on brain measures. I used FreeSurfer v5.3 (freesurfer-x86_64-unknown-linux-gnu-stable5-20130513) and the mask_face function developed for XNAT (Milchienko & Marcus, 2013) with the default normalized filter. The masks were not invasive and did not overlap with brain tissue.
I compared output of the recon-all between T1 scans with and without masked face for a small sample. I found high correlations between the output of the two scans (extracted values: cortical thickness, surface area, (sub)cortical volume, global values). Slight differences seem to occur from the start of the recon-all (talairach transform). Adding ear masks to the face-masked scans, made the differences smaller (i.e. higher correlations with raw scans). Also, the recon-all run time appears to be reduced.
Could you explain how face and ear information is used in the recon-all and why adding ear masks to masked-face scans might reduce run-time and improve reliability? Could it be the case that skull stripping is easier without ears for example? Thank you in advance.
Kind regards, Elizabeth
-------------------------------------------------------- Elizabeth Buimer, Research Assistant Department of Psychiatry, UMC Utrecht Room: A.01.161 e.e.l.buimer@umcutrecht.nl
------------------------------------------------------------------------------
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
------------------------------------------------------------------------------
This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197.
Please consider the environment before printing this e-mail.