Hi,
Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Natalie Busby <natalie.busby@manchester.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 31, 2016 at 9:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all Exiting without Error

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

 

 

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