Hello Lilla,

Many thanks for you kind and helpful respond! We have just applied for the code for the infant pipeline and would be happy to utilize it.

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

Von: <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von "Zollei, Lilla,Ph.D." <LZOLLEI@MGH.HARVARD.EDU>
Antworten an: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Datum: Dienstag, 4. August 2020 um 22:56
An: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Schülke-Gerstenfeld, Markus" <markus.schuelke@charite.de>
Betreff: [ext] Re: [Freesurfer] recon-all error

Hi Nina,

The recon all pipeline uses an adult atlas. We have had collaborators successfully using it with subjects all the way down to age 4.5yrs, but under that it would not be recommended. Have you looked at the infant pipeline?

Best, Lilla

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wilpert, Nina- Maria <nina-maria.wilpert@charite.de>
Sent: Tuesday, August 4, 2020 10:51 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Schülke-Gerstenfeld, Markus <markus.schuelke@charite.de>
Subject: [Freesurfer] mri: recon-all error

External Email - Use Caution

Hello FreeSurfer Developers,

We are attempting to run the command recon-all on pediatric MRI images (1-13 yrs), 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, 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….”

Would you 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!