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

Question List

Answers to May 2014 Course questions:

Topic: Gray Matter Volume
Question: In v5.0 and above, there is a stat within each subject's stat folder that is a single value for whole brain gray matter volume. Two questions regarding that metric: 1) Does that include the cerebellum? 2) Is there a way to access that statistic using version 4.5?

Answer: 1) yes 2) I would run v5.3 mri_segstats to get an up-to-date aseg.stats file.
Doug Greve

Topic: Control points
Question: I use control points followed by autorecon to include areas that are obviously part of the brain but were not included in the first run. how many times should i do this, because sometimes i do it like 8 or 10 times (with added control points) and that area is still excluded, is there another way of doing this?

Answer: There are a couple of possibilities. Have you checked the wm.mgz to make sure that is filled in for every voxel you think is white matter? If not, fill that in and try rerunning (possibly without the control points).

Also, if control points are not placed on voxels that are less than 110, then you might not see the desired effect. It could also be that you are not placing enough control points on enough slices.

Without seeing your case, I can't say for sure what you need but most cases need 3-4 control points on every other slice for several slices. Since control points are used for fixing intensity problems, you'll need to place them on most of the slices that have low intensity in that region and not necessarily just on the slices that have problems with the surface.

If control points were placed in gray matter, partial volumed voxels, or white matter bordering gray matter, that could be causing the problem. You should delete those control points.

If after trying the above, control points still don't seem to be working, let us know which version you are working with so we can investigate.

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.