Dear FreeSurfer team,

I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing.

The data i'm working with is already resliced to 1 mm and co-registered in MNI-space.

1) Can i use this data or would it be preferable to use the original T1's?

My thought was to run the following command:

recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all

2) Does this look correct? Is there anything i should be aware of?

3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1?

4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing?

5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer?

Best, Silas