External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace each voxel labeled as hippo by the label of the closest, non-hippocampal structure. 4. Paint your hippocampi from step 2 on the hippocampal-less aseg. I hope this helps, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13/06/2018, 17:18, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lara Foland-Ross" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of lfol...@stanford.edu> wrote: External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippocampus. Final volumes of manually edited hippocampi were submitted to a repeated measures ANOVA which showed a significant main effect of diagnosis on the overall size of this structure (controlling for age and TBV). We recently submitted this paper and just received a request from a reviewer that asked that we run a subfield analysis on these data to better understand the regions driving this overall effect. What I'd like to know is: would the subfield approach *not* be recommended on this dataset considering that artifacts necessitated a good deal of manual intervention for the entire region? Second, if it a subfield approach *is* okay to run on these data, how can I feed in my manually edited volumes to ensure that the corrected segmentations of the entire hippocampus is used during subfield creation? thanks very much in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795 _______________________________________________ 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
