New subject: Recon-all Exiting without Error

31 Oct 2016


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