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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