| Hi, I am trying to get TRACULA running. I have converted the DTI data using dcm2nii (as i was unable to get tracula to read the .ima Siemens DICOM) and have a bevc and bval file output from dcm2nii. The error I get is in bold below (from trac-all.log). I believe that the error is coming from the bevy/bval file however I can’t see what the issue is with the data contained within the file. Does the output from dcm2nii need to be reformatted for input to TRACULA ? Cheers, Scott ------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue 7 Apr 2015 21:43:25 AEST mri_convert /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz mri_convert /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz... TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99802, 0.0188805, 0.0599977) j_ras = (0.0278771, 0.987856, 0.152851) k_ras = (0.0563831, -0.154221, 0.986426) writing to /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz... cp /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bvec.txt /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs cp /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bval.txt /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals flip4fsl /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -9.38889 fslswapdim /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz x y z /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz INFO: found /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvecs /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvecs mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvals /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvals mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz ln -sf /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/data.nii.gz mri_concat --i /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz --mean --o /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/lowb.nii.gz niiRead(): error opening file /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz Darwin Scotts-MacBook-Pro.local 14.1.0 Darwin Kernel Version 14.1.0: Thu Feb 26 19:26:47 PST 2015; root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64 |
dwi_orig.mghdti.bvals
Description: Binary data
dwi_orig.mghdti.bvecs
Description: Binary data
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