Hello,
I’m new to mrtrix and been having issues with dwifslpreproc
The data I want to process is 64 DWI volumes of B=1000 in both directions (AP and PA) and each have and initial B0 volume.
First I concatenated the data into all_dwi.mif (130 volumes) and did the denoising and degibbs steps.
Then i tried running the code:
dwifslpreproc dwi_degibbs.mif dwi_preproc.mif -info -nocleanup -rpe_all -pe_dir AP -eddy_options " --slm=linear"
to wich I get the following error
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc:
dwifslpreproc: Loading header for image file '/home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwi_degibbs.mif'
dwifslpreproc: Generated scratch directory: /home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwifslpreproc-tmp-NHVM08/
Command: mrconvert /home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwi_degibbs.mif /home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwifslpreproc-tmp-NHVM08/dwi.mif -json_export /home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwifslpreproc-tmp-NHVM08/dwi.json
mrconvert: [ 0%] copying from "/home/brai.../sub-01/dwi/dwi_degibbs.mif" to "/home/brai.. mrconvert: [100%] copying from "/home/brai.../sub-01/dwi/dwi_degibbs.mif" to "/home/brai...lpreproc-tmp-NHVM08/dwi.mif"
dwifslpreproc: Changing to scratch directory (/home/brain_smc/Documentos/Grav_Neg/Nifti/sub-01/dwi/dwifslpreproc-tmp-NHVM08/)
dwifslpreproc: Loading header for image file 'dwi.mif'
dwifslpreproc: Command: '/home/brain_smc/anaconda3/bin/mrinfo dwi.mif -shell_indices' (piping data to local storage)
dwifslpreproc: Result: 0,65 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129
dwifslpreproc: Command: '/home/brain_smc/anaconda3/bin/mrinfo dwi.mif -shell_bvalues' (piping data to local storage)
dwifslpreproc: Result: 0 1000
dwifslpreproc: [ERROR] Unable to determine matching reversed phase-encode direction volume for DWI volume 4
I’ve already tried different approaches suggested in this forum, such as to run the 64 volumes seperate to the B0 and the B0 in the -se_epi flag but was unsuccessful in solving the problem.