Dear TRACULA experts
Hello. I am running TRACULA, but it exited an error very early in pre-processing. My data is not a format in DICOM but .nii, does this cause the error? I set the dcmlist to .nii file (in attachment).
Could anyone help me? This is the error log and I attached the configuration file.
-error log-
[watanabeanris-Mac-Pro:mybook/Anri/diffusion_tutorial] watanabeanri% trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons
INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/dmrirc.local -log /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.log -cmd /volumes/mybook/Anri/diffusion_tutorial/HC_025/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Aug 22 11:03:45 JST 2014
mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz
mri_convert /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /volumes/mybook/Anri/diffusion_tutorial/HC_025/orig/00.nii...
TR=7175.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996496, -0.0735924, -0.0397398)
j_ras = (-0.0756091, 0.995787, 0.0518831)
k_ras = (-0.0357542, -0.0547061, 0.997862)
writing to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz...
cp /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs
flip4fsl /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8
fslswapdim /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.nii.gz x y z /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz
INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs
mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals
mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory
Darwin watanabeanris-Mac-Pro.local 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Aug 22 11:03:46 JST 2014
Many thanks for your help.
Best Wishes, Anri WATANABE
********************************************************************** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************