Hello!
I'm having problems running the trac-all -tensor step. dtifit appears to run correctly; the problem seems to be in mapping the output files to the template space. The command I run is:
trac-all -tensor -c /cluster/manoach/dod/BU_pipeline/data/DOD_DODCON004/tracula.cfg
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And the error I get is (the move file doesn't exist, but dtifit_FA.nii.gz does exist):
mri_vol2vol --mov /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz --targ /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz --o /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii.gz --m3z /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35.m3z --noDefM3zPath --interp trilin --no-save-reg
niiRead(): error opening file /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz
Using the m3z file as it is; no assumed location.
movvol /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/anatorig/dtifit_FA.flt.nii.gz
targvol /autofs/cluster/manoach/dod/subjects/cvs_avg35/mri/norm.mgz
outvol /cluster/manoach/dod/BU_pipeline/data/DODCON004/dmri/cvs/dtifit_FA.flt.nii.gz
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilin (1)
precision float (3)
Gdiag_no -1
Morphing
InvertMorph 0
Synth 0
SynthSeed 1381542765
Linux huygens 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Sun Oct 6 12:04:16 EDT 2013
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And here is the output of bugr:
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.4 (Final)
Kernel info: Linux 2.6.32-358.2.1.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /cluster/manoach/dod/subjects
PWD: /cluster/manoach/dod/BU_pipeline/dti_scripts
ssh huygens
setenv SUBJECTS_DIR /cluster/manoach/dod/subjects
cd /cluster/manoach/dod/BU_pipeline/dti_scripts
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Additionally, the subject is DODCON004 and the script directory can be found at /cluster/manoach/dod/BU_pipeline/data/DODCON004/scripts
Thanks for your help! Any advice would be appreciated.
Jenn Segawa