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 **********************************************************************
Hi Anri - What text editor did you use to create the configuration file? It looks like the last line (which specifies the b-value file) has no end-of-line, and so that line is not executed, hence the failure to find the b-value file. Can you please press "enter" at the end of that line, so that you move to the next line, then save the configuration file and try again?
a.y
On Fri, 22 Aug 2014, 渡辺杏里 wrote:
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
Thanks, Anastasia. I did as you told me, and I could run preprocessing without error! Thank you so much!!
Anri
********************************************************************** 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 **********************************************************************
2014-08-25 19:23 GMT+09:00 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:
Hi Anri - What text editor did you use to create the configuration file? It looks like the last line (which specifies the b-value file) has no end-of-line, and so that line is not executed, hence the failure to find the b-value file. Can you please press "enter" at the end of that line, so that you move to the next line, then save the configuration file and try again?
a.y
On Fri, 22 Aug 2014, 渡辺杏里 wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Anastasia Yendiki -
渡辺杏里