Hi Florent, See for answers below. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of k3ops@free.fr k3ops@free.fr Sent: Friday, October 2, 2020 4:30 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Infant FreeSurfer issues

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Hi FreeSurfer team,

I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks now on infants from 0.4 to 5.4 years-old.

I know Infant FreeSurfer is recommended for 0-2 years old infant but standard FreeSurfer was failing due to many lacunar infarcts in the white matter. So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 years-old subjects and results look good. I know standard FreeSurfer has been tested on infant from 4.2 years-old, so what would be your recommendation for subjects from 2 to 4.2 years old?

** That is an age range that we are trying to cover at the moment, but we do not have a specific atlas representing that age range. If the infant pipeline works for you, that is great.

Have you already run Infant FreeSurfer on subjects older than 2 years-old?

** No, we do not recommend it.

I also have some processing issues with my actual data: 1. Pixels with 0 value => probably out of the brainmask so the pixels are set to 0 after masking So, sometimes lateral ventricles are miss-segmented (https://ibb.co/JpWG9st) ** If there is no intensity value there, it is as if that area was masked out so there is not going to be a label assigned to that area.

2. Thalamus region is missing from the aseg stat export (always equal to 0 mm3), do you have a fix? Should I fix a LUT file? ** The pipeline that you are using is still labeling the thalamus with an old label value. You could switch the labels to the current ones and rerun the stats file generation or I can send you an updated script. Below are the steps from the mri dir that can change the labels:

mri_binarize --i aseg.mgz --replace 48 49 --replace 9 10 --o aseg.corrected.mgz rm aseg.mgz ln -s aseg.corrected.mgz aseg.mgz

3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native space.

** We do not work in the MNI space. Can you give me more details about what you are trying to do?

4. Do you have any workaround for large ventricles segmentation issue (https://ibb.co/nnbZcYs)? Standard FreeSurfer has a -bigventricle option, do you have a similar approach?

** We do not yet have such a flag for infants.

And some additional questions: • brainstem seems to be split into multiple sub-regions, is it possible get the entire brainstem volume in the aseg stat export?

** You would need to do it manually and merge the labels of interest.

• I saw that corpus callosum is not present in the “aseg” segmentation, so is this region out of the Infant FreeSurfer atlases?

** With the most recent script, it is.

• Is it possible to get the mean cortical thickness for the labels you are providing?

** Yes, they should all be in the surface stats files.

Many thanks as I know there are plenty of questions here :) Best, Florent

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