Hi Lara,
the longitudinal pipeline is designed for adults with the assumption
that head size is fixed. We are working on a new pipeline that will
allow processing of images from children, but that will take a while.
Especially considering that there will be large differences in the brain
as well as the head size between age 2 and age 10, I recommend to only
use the cross sectional pipeline for this data.
Best, Martin
On 01/13/2016 12:05 PM, Lara Foland-Ross wrote:
Dear Freesurfer experts,
I am working on a longitudinal analysis of cortical structure and am
experiencing some errors with registration. I have 3 timepoints for each
participant:
time 1: age 2
time 2: age 5
time 3: age 10
Time 1 and 2 are from a 1.5T scanner. Time 3 is from a 3T scanner.
Despite the age range and scanner difference, the registrations in the
longitudinal pipeline (I'm using version 5.3) are performing relatively well.
However, in comparing the LONG outputs slice by slice, it appears that in a
majority of my subjects, there are some minor mismatches in brain anatomy. An
example is attached here (minor_reg_error.jpg).
In other instances, there are more substantial registration errors. Again,
example attached here (major_reg_error.jpg).
My question is how much mismatch is acceptable? And how can I go about fixing
poor registrations in subjects who have significant errors in alignment?
Many thanks in advance,
Lara
Lara Foland-Ross, Ph.D.
Research Associate
Center for Interdisciplinary Brain Sciences Research
Stanford University School of Medicine
401 Quarry Road, Room 1356
Stanford, CA 94305-5795
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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