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.

Steps in analysis:

1) First steps of recon-all:

recon-all -autorecon1 -autorecon2

2) Reslicing the FLAIR images:

The aseg.auto.mgz (256x256x256) didn't have the same size as the FLAIR (resliced to 1mm, co-registered in MNI-space and with manually drawn binary lesion masks (218x182x182)). I overcome this problem by reslicing the FLAIR images using aseg.auto.nii as the image defining space. This was done in SPM8, and prior to this the aseg.auto.mgz was converted to a .nii using mri_convert.  

3) Insert lesions from the resliced FLAIR images to aseg.mgz:

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

4) The last steps of recon-all:

recon- all -autorecon2-cp -autorecon3

When running the following command i get this error: 

............

The lesions looks alright (as if they are in the right place). Do you have any suggestions what to do if they are not? And what could be the problem if they are placed correctly?

What is the advantage of starting by running autorecon-1 and 2 and then inserting the lesions from the FLAIR?

Thanks a lot for all your help!

Best, Silas