Hi Liliana - This error indicates that it could not find the /home/lapsi/test/bvals file at all, not that the file had the wrong format. Does that file exist?
Also, if you run "trac-all -prep -noqa", you're telling trac-all NOT to do the QA step that calculates the motion measures, so I'm confused about what exactly you ran. The log file from scripts/trac-all.log should show you what steps were run and what the command line was.
a.y
On Wed, 22 Jan 2014, Liliana Maia wrote:
Hi,
Within the new Tracula update and with outputs resulted from trac-all -prep -noqa I ran:
dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'
And an error message appears:
machine x86_64
Output motion measure file: /home/lapsi/test/motion.txt Input transform file: /home/lapsi/test/dwi.ecclog Input DWI file: /home/lapsi/test/dwi_orig.nii.gz Input b-value table: /home/lapsi/test/bvals Low-b image intensity threshold: 100 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 33 volumes Loading DWI volume series from /home/lapsi/test/dwi_orig.nii.gz Loading b-value table from /home/lapsi/test/bvals ERROR: Could not open /home/lapsi/test/bvals for reading
I tried with the b-values one value for each line in file bvalsT (see attachments): dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog' ,but the same error occurred.
What can I do to verify this head motion?
Thank you Best,
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Liliana Maia MEng Biomedical Engineering