Hello FreeSurfer Developers,

 

We are attempting to run the command recon-all on pediatric MRI images, as described on your website:

cmd=”recon-all -i $Dir/*.nii.gz -s sub02_test  -all”

 

The command worked well for some of our subjects. For others (#2 3 years, 1 months; #6 6 years, 10 months; #3 9 years, 4 months), however, hard failures occurred and recon-all did not finish or we received the following error (please find the recon-all.log attached):

“recon-all -s sub02_reconall exited with ERRORS at….”

 

We are well aware that the adult Freesurfer pipeline is not recommended for children under the age of 4 years and the recently published infant Freesurfer pipeline is to be used instead. Since subject#6 and #3 and well above this age, however, we wanted to ask whether you would have any recommendations on how to trouble-shoot these issues? We have attached the recon-all.log documents in case it's of any use.

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Linux

4) recon-all.log: see attached.

 

We would very much appreciate your help!

 

Kind regards,

Nina Wilpert

 

 

 

Nina-Maria Wilpert | medical student
T +49 (0) 30 450559858 | M +49 (0) 15783851445
E nina-maria.wilpert@charite.de

Department of Neuropediatrics

Charité, Universitätsmedizin Berlin

Institute of Anatomy

University of Leipzig

Genetics and Development of the Cerebral Cortex

Hôpital Necker-Enfants malades & IMAGINE, Paris