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Dear Freesurfer experts,

I am running recon all from the terminal of a linux machine: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I tried recon all on an image dataset of small vessel disease patients. I tried the command on several subjects and I got the same outcome: a soft fallure.

Please, find the recon all log in the attachment.

Even though in the "recon all.log": it says: recon-all -s sub025 finished without errors, after checking the pial and white matter segmentations, very clear misplacement failures and part of dura mater are present (see attachment: segmenation misplacement and dura).

I am also wandering how to avoid that white matter lesions are taken into the aseg segmentation?

I checked the documentation and this kind of errors is not mentioned anywhere. Can be the case, that this error is due to the fact that these are clinical images? Can this problem be fixed? 

For sake of curiosity, I tried the recon all command on another dataset (stroke) and with these data I got an hard failure.

recon all exited with errors:

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second recon all o35403143 with errors)

Please, can anyone give me some ideas how to fix both errors?

Thank you in advance

Ileana