This wiki page contains the students questions and answers from the November 2013 Freesurfer course.

Question List

Answers to May 2014 Course questions:



Questions from previous courses:

Topic : 1.5 and 3T longitudinal data

Question: I have a set of longitudinal data that began on a 1.5T scanner but then our research group moved to a 3T scanner exclusively. Is it possible to use longitudinal analysis in FreeSurfer to analyze both 3T and 1.5T data in the same analysis or possibly smooth across both to accomplish this analysis?

Yes, you can add the scanner type as a time varying covariate into a linear mixed effects model. It would be good to have several time points before and after the change to get more reliable slope estimates on both sides. See also LinearMixedEffectsModels .


Hello, I would like to know how to measure the cerebellar vermis volume using freesurfer. As far as I know, freesurfer provide cerebellum cortex volume and cerebellum white matter volume in the aseg.stats file, but I could not find cerebellar vermis volume. Can freesurfer provide cerebellar vermis volume? I found a web page in freesurfer wiki that describe cerebellum parcellation. I hope to obtain the volume of each subregion of cerebellum, but I have not understood the procedure. I know the MNI152 atlas is in the $FREESURFER_HOME/average/ directory. Could you tell me how to warp the MNI152 parcellations to subjects' native structural MRI space and extract the volume of each subregion? Thanks in advance.

We do not segment the cerebellar vermis. If you want to measure it or label it, you will need to manually draw it on each of the subjects or if you find another atlas with the required label, register that to your subject and project the label to that space. The cited URL provides cerebellar clustering in the MNI152 nonlinear space. You need to use the talairach.m3z transformation to map the labels back to the subject's native space.

I know freesurfer can process cortical surface correctly for the subjects who are over 5 years old. How do you think the reliability of the freesurfer outputs in very young children (e.g. 3-4 years old).

Not good. We do not encourage people to use FS recon for that age group. We do not have a qunatifiable performance measure though.