Hi,

I have just started using FreeSurfer and I am trying to do the subcortical segmentation on some Human Connectome Data.

In the command line I typed,

‘recon-all –i T1w_acpc_dc_restore_1.25.nii –subjid 100307’

The following output was produced:

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects

Actual FREESURFER_HOME /usr/local/freesurfer

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux

/usr/local/freesurfer/subjects/100306

mri_convert /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii...

TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz...

#------------------------------------------

Started at Mon Oct 31 10:12:26 EDT 2016

Ended at Mon Oct 31 10:12:31 EDT 2016

#@#%# recon-all-run-time-hours 0.001

recon-all -s 100306 finished without error at Mon Oct 31 10:12:31 EDT 2016

done

I was wondering if you knew what the problem was?

Thank you!

Best wishes,

Natalie