That recon-all command will not work as the FLAIR input should be a simple FLAIR image. The FLAIR will only correct the pial surface and will have nothing to do with lesion segmentation. Emily Lindermer has a tool that can take a T1 and FLAIR and produce a lesion map; but given that you already have manual segmentations, maybe that is not so helpful. One thing you can do is to edit the aseg.mgz to insert your lesions. First run recon-all with -autorecon1 -autorecon2 instead of -all. Then, in matlab,

aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg

manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever format, but should be binary

ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);

newaseg = aseg;

newaseg.vol(ind) = 77;

MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so make a backup

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? -> update: Does this command only improve the pial surface? How can i also improve the white mater segmentation (white) using FLAIR corrections?

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

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