This is a known issue. The patch for the mri_segstats binary can be found here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mri_segstats.centos6_x86_64

Please overwrite your existing mri_segstats binary with the one from the link above.

On 06/26/2017 02:26 PM, Shuo Zhou wrote:

Hello FreeSurfer Developers,

I am using recon-all to process the structural mri data. The autorecon1 works fine, however I got the following error when I run the recon-all autorecon2 command:

mghRead(/home/acp16sz/openfmri/data/subdir/ds003_sub001/mri/ribbon.mgz, -1): could not open file.

I have checked the output of the recon-all steps (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable), the file ribbon.mgz is the output of autorecon3, why it is required in autorecon2. Also, Ive attached the recon-all.log in case it's of any use.

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2. Platform: 64-bit Scientific Linux (which is Redhat based) HPC

3. uname -a: Linux iceberg-login2 2.6.32-696.3.2.el6.x86_64 #1 SMP Mon

Jun 19 11:23:31 CDT 2017 x86_64 x86_64 x86_64 GNU/Linux

4. recon-all.log: see attached

Kind regards,

Shuo

Sent from Mail https://go.microsoft.com/fwlink/?LinkId=550986 for Windows 10

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