I’m really sorry,

I’ve just realised there is an error in the naming structure in /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/

That is probably the cause – not sure why that happened will sort it out and try again – sorry!

From: Justin McKee <justin.mckee@ndcn.ox.ac.ukmailto:justin.mckee@ndcn.ox.ac.uk> Date: Monday, 12 October 2015 21:54 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: error with .lta files in longitudinal

Hi,

I’ve not idea why a few of my longitudinal runs have started to fail. It’s saying there’s a problem with the .lta files,

From “bugr” script

FREESURFER_HOME: /opt/fmrib/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64

I ‘ve lost the exact command line but it would have been

recon-all –long ACT_364_12M ACT_364_3scan_base -all

The error message is

mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz

mri_convert -at /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta -odt uchar -rt cubic /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M.long.ACT_364_3scan_base/mri/orig.mgz ltaReadFile(/home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta): can't open file $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fs0/jmckee/scratch/fs_dir/ACT_364_12M/mri/orig/001.mgz... TR=1000.00, 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) INFO: Reading transformation from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ACT_364_12M_to_ACT_364_3scan_base.lta Linux jalapeno12.fmrib.ox.ac.uk 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ACT_364_12M.long.ACT_364_3scan_base exited with ERRORS at Mon Oct 12 18:16:19 BST 2015

I’m a bit confused because /home/fs0/jmckee/scratch/fs_dir/ACT_364_3scan_base/mri/transforms/ Has a full complement of.lta files including the one mentioned in the error message..

Obviously it’s taken a while to get to this stage so I’m loathe to re-run the –base and –long again, as I had made extensive edits to the ACT_364_3scan_base brain mask file and ran autorecon-pial and don’t want to loose those if possible, or indeed do them again and get the same mistake at this stage. Have attached the recon-all.log file

Any help gratefully received!

Cheers

Justin

Dr Justin McKee Clinical Research Fellow in Multiple Sclerosis Nuffield Department of Clinical Neuroscience University of Oxford