It sounds like a bad file name or path.
Check everything is where you say it is and has the same suffix that you are entering into the command.
Liam.
*******************************************
Liam Nestor, Ph.D
Office C8-523
Laboratory for Molecular Neuroimaging
Semel Institute for Neuroscience and Human Behavior
760 Westwood Plaza
Los Angeles 90024
Tel: 310-206-0655
E-mail: [log in to unmask]
*******************************************
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Jayanth Kolar [[log in to unmask]]
Sent: Monday, March 09, 2009 2:41 PM
To: [log in to unmask]
Subject: [FSL] SIENAX error
Hello,
When I'm trying to run SIENAX with 512x512 matrix image, I get a following error. Does anyone have an idea what is wrong?
I'm running the FSL on Windows PC (total 4GB RAM; 3 GHz processor).
By the way it is working fine if I'm running it with 256x256 images, but the error doesn't seem like memory problem.
Thank you so much.
Command:
=======
[fsl@localhost temp2]$ sienax 20070803_162423E12539S16I1csfnoam12Pang-yuTangs016a1001.nii.gz -o ResultSienax_PTcsf_bet2_035 -B "-R -f 0.35"
Output:
======
/home/fsl/fsl/bin/sienax: line 285: 7294 Aborted ${FSLDIR}/bin/fast -g $imtype $segopts ${I}_stdmaskbrain >>report.sienax 2>&1
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
Error: failed to open file I_stdmaskbrain_pve_1
ERROR: Could not open image I_stdmaskbrain_pve_1
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_2'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_2): bad header info
Error: failed to open file I_stdmaskbrain_pve_2
ERROR: Could not open image I_stdmaskbrain_pve_2
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_2
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_seg'
** ERROR: nifti_image_open(I_stdmaskbrain_seg): bad header info
Error: failed to open file I_stdmaskbrain_seg
ERROR: Could not open image I_stdmaskbrain_seg
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/fsl/bin/sienax: line 289: 7889 Aborted ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_seg 1.9 5 ${I}_render
** ERROR (nifti_image_read): failed to find header file for 'I_render'
** ERROR: nifti_image_open(I_render): bad header info
Error: failed to open file I_render
ERROR: Could not open image I_render
Image Exception : #22 :: Failed to read volume I_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/home/fsl/fsl/bin/sienax: line 290: 7894 Aborted ${FSLDIR}/bin/slicer ${I}_render -s 1 -x 0.4 gr${I}a.png -x 0.5 gr${I}b.png -x 0.6 gr${I}c.png -y 0.4 gr${I}d.png -y 0.5 gr${I}e.png -y 0.6 gr${I}f.png -z 0.4 gr${I}g.png -z 0.5 gr${I}h.png -z 0.6 gr${I}i.png
Cannot open grIa.png for reading
/home/fsl/fsl/bin/sienax: line 291: 7895 Segmentation fault ${FSLDIR}/bin/pngappend gr${I}a.png + gr${I}b.png + gr${I}c.png + gr${I}d.png + gr${I}e.png + gr${I}f.png + gr${I}g.png + gr${I}h.png + gr${I}i.png ${I}_render.png
/bin/rm: cannot remove `grI?.???': No such file or directory
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/home/fsl/fsl/data/3D_Volume_studies_AARON/temp2/ResultSienax_PTcsf_bet2_035/report.html
Estimated normalised brain volume (NBV) =
2.58
[fsl@localhost temp2]$
--
Jayanth Kolar
Graduate Research Assistant
Physiological Imaging and Modeling Lab
University of Illinois at Chicago
Chicago IL - 60607
1-408-398-0097
http://www.ece.uic.edu/~jkolar
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