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

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