Re: [Freesurfer] hippocampus subfields and manual editing - Freesurfer

13 Jun 2018

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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-bounces@nmr.mgh.harvard.edu on behalf of Lara Foland-Ross" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of lfoland@stanford.edu> wrote:

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    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

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