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MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
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Alternative phase encoding schemes #66

Closed araikes closed 1 year ago

araikes commented 1 year ago

I'm working on a large database that includes DWI acquisitions (multi-session, multi-site, over about a decade). None of the data was acquired with a reverse phase-encoded image and some of the later data has main phase encoding direction P>>A. When this is the case, micapipe behaves poorly and attempts to use the same image for the dwi_rpe file (see below). There is no option to specify that there is no reverse phase encoded image.

I can trick/coerce it into working by giving it a non-existent file name (e.g., -dwi_rpe /nifti/nothing.nii.gz), but this seems less than ideal as a solution.

[adamraikes@r5u25n1 rush]$ singularity run --cleanenv --nv -B /xdisk/adamraikes/rush/nifti:/nifti:ro -B /xdisk/adamraikes/rush/derivatives:/xdisk/adamraikes/rush/derivatives -B /tmp:/tmp -B /groups/adamraikes/license.txt:/opt/freesurfer-6.0.0/license.txt /groups/adamraikes/singularity_images/micapipe_0.1.5.2.sif -bids /nifti -out /xdisk/adamraikes/rush/derivatives/micapipe -sub 00228190 -ses 07 -tmpDir /tmp -proc_dwi -dwi_main /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz -b0thr 61 -threads 8
INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (875) bind mounts
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /opt/freesurfer-6.0.0
FSFAST_HOME       /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /opt/freesurfer-6.0.0/subjects
MNI_DIR           /opt/freesurfer-6.0.0/mni
FSL_DIR           /opt/fsl-6.0.3

[ WARNING ]..... DEPRECATION: mica-pipe is deprecated and will be removed from upcoming versions (use micapipe instead) 

micapipe -bids /nifti -out /xdisk/adamraikes/rush/derivatives/micapipe -sub 00228190 -ses 07 -tmpDir /tmp -proc_dwi -dwi_main /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz -b0thr 61 -threads 8

-------------------------------------------------------------
    MICA pipeline - (Version v0.1.5 'Roadrunner') 
        Subject: 00228190 Session: ses-07
-------------------------------------------------------------

[ WARNING ]..... fix was not found, ICA-FIX will be skipped 

[ INFO ]..... micapipe will use 8 threads for multicore processing 

[ INFO ]..... Subject 00228190 directory exist 

[ INFO ]..... Inputs of proc_dwi: 
        tmpDir        : /tmp
        dwi_main      : /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz
        dwi_rpe       : DEFAULT
        rpe_all       : FALSE
        dwi_acq       : DEFAULT
        Affine only   : FALSE
        B0 threshold  : 61
        bvalue scaling: DEFAULT
        Processing    : LOCAL
/opt/micapipe/functions/02_proc-dwi.sh: line 100: micapipe_check_dependency: command not found

-------------------------------------------------------------
    Diffusion Weighted Imaging processing
        micapipe v0.1.5 'Roadrunner', LOCAL
-------------------------------------------------------------

[ INFO ]..... MICA pipe - Software versions 
        MRtrix3.....    3.0.1
                        /opt/miniconda-latest/envs/micapipe/bin/mrinfo
        FSL.........    6.0
                        /opt/fsl-6.0.3
        ANFI........     Feb 13 2023 (Version AFNI_23.0.04 'Commodus')
                        /opt/afni-latest/3dresample
        ANTS........     2.3.3.dev168-g29bdf
                        /opt/ants-2.3.4
        WorkBench...    1.3.2
                        /usr/bin/wb_command
        FreeSurfer..    freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
                        /opt/freesurfer-6.0.0
        fix.........    
                        /opt/fix
        python......    Python 3.7.12
                        /opt/miniconda-latest/envs/micapipe/bin/python
        R...........    3.6.3
                        /usr/bin/R

[ INFO ]..... Variables for DWI processing 
        proc_dwi dir    :   /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi
        bids_dwis       :   N-1, /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz
        dwi_reverse     :   N-1, /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz
        T1 nativepro    :   
        T1 5tt          :   
        MNI152_mask     :   /opt/micapipe/MNI152Volumes/MNI152_T1_0.8mm_brain_mask.nii.gz

[ INFO ]..... Saving temporal dir: FALSE 

[ INFO ]..... ANTs and MRtrix will use 8 threads 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:34 MST 2023:
COMMAND -->   mkdir -p /tmp/6145_micapipe_proc-dwi_00228190  

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:34 MST 2023:
COMMAND -->   cd /tmp/6145_micapipe_proc-dwi_00228190  

[ INFO ]..... DWI denoise and concatenation 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:34 MST 2023:
COMMAND -->   mrconvert /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz -json_import /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.json -fslgrad /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.bvec /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.bval /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif   
mrconvert: [100%] uncompressing image "/nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz"
mrconvert: [100%] copying from "/nifti/sub...90_ses-07_dir-PA_dwi.nii.gz" to "/tmp/6145_...28190_ses-07_dir-PA_dwi.mif"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:35 MST 2023:
COMMAND -->   dwiextract /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif -bzero  
dwiextract: [100%] extracting volumes

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:35 MST 2023:
COMMAND -->   mrmath /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif mean /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.nii.gz -axis 3 -nthreads 8  
mrmath: [100%] preloading data for "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif"
mrmath: [100%] computing mean along axis 3...
mrmath: [100%] compressing image "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.nii.gz"

[ INFO ]..... Concatenatenating shells 

[ INFO ]..... DWI MP-PCA denoising and Gibbs ringing correction 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:35 MST 2023:
COMMAND -->   dwidenoise /tmp/6145_micapipe_proc-dwi_00228190/dwi_concatenate.mif /tmp/6145_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif -nthreads 8  
dwidenoise: [100%] preloading data for "/tmp/6145_micapipe_proc-dwi_00228190/dwi_concatenate.mif"
dwidenoise: [100%] running MP-PCA denoising
mrcalc: [100%] computing: (/tmp/6145_micapipe_proc-dwi_00228190/dwi_concatenate.mif - /tmp/6145_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif)
mrmath: [100%] preloading data for "/tmp/mrtrix-tmp-txVukE.mif"
mrmath: [100%] computing mean along axis 3...

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:28:51 MST 2023:
COMMAND -->   mrdegibbs /tmp/6145_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_space-dwi_desc-MP-PCA_dwi.mif -nthreads 8  
mrdegibbs: [100%] performing Gibbs ringing removal
mrcalc: [100%] computing: (/tmp/6145_micapipe_proc-dwi_00228190/MP-PCA_dwi.mif - /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_space-dwi_desc-MP-PCA_dwi.mif)
mrmath: [100%] preloading data for "/tmp/mrtrix-tmp-Tqiga4.mif"
mrmath: [100%] computing mean along axis 3...

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrinfo /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_space-dwi_desc-MP-PCA_dwi.mif -json_all /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_space-dwi_desc-MP-PCA_dwi.json  

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrinfo /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_desc-MP-PCA_residuals-dwi.mif -json_all /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_desc-MP-PCA_residuals-dwi.json  

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrinfo /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_desc-deGibbs_residuals-dwi.mif -json_all /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_desc-deGibbs_residuals-dwi.json  

[ INFO ]..... DWI reverse phase encoding processing: sub-00228190_ses-07_dir-PA_dwi 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrconvert /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz -json_import /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.json -fslgrad /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.bvec /nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.bval /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif   
mrconvert: [100%] uncompressing image "/nifti/sub-00228190/ses-07/dwi/sub-00228190_ses-07_dir-PA_dwi.nii.gz"
mrconvert: [ERROR] output file "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif" already exists (use -force option to force overwrite)
mrconvert: [ERROR] error creating image "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   dwiextract /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi.mif /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif -bzero  
dwiextract: [ERROR] output file "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif" already exists (use -force option to force overwrite)
dwiextract: [ERROR] error creating image "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrmath /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif mean /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.nii.gz -axis 3 -nthreads 8  
mrmath: [100%] preloading data for "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.mif"
mrmath: [ERROR] output file "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.nii.gz" already exists (use -force option to force overwrite)
mrmath: [ERROR] error creating image "/tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_dir-PA_dwi_b0.nii.gz"

[ INFO ]..... DWI-rpe: concatenatenating shells 

[ INFO ]..... DWI-rpe: MP-PCA denoising and Gibbs ringing correction 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:00 MST 2023:
COMMAND -->   mrdegibbs /tmp/6145_micapipe_proc-dwi_00228190/rpe-MP-PCA_dwi.mif /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_dir-rpe_desc-MP-PCA_dwi.mif -nthreads 8  
mrdegibbs: [100%] performing Gibbs ringing removal

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:08 MST 2023:
COMMAND -->   mrinfo /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_dir-rpe_desc-MP-PCA_dwi.mif -json_all /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_dir-rpe_desc-MP-PCA_dwi.json  

[ INFO ]..... DWI dwifslpreproc 

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:09 MST 2023:
COMMAND -->   mrconvert /tmp/6145_micapipe_proc-dwi_00228190/sub-00228190_ses-07_space-dwi_desc-MP-PCA_dwi.mif /tmp/6145_micapipe_proc-dwi_00228190/dwi_dns_even.mif -coord 0 0:127 -coord 1 0:127 -coord 2 0:79 -coord 3 0:end -force  
mrconvert: [WARNING] existing output files will be overwritten
mrconvert: [100%] copying from "/tmp/6145_...ace-dwi_desc-MP-PCA_dwi.mif" to "/tmp/6145_...i_00228190/dwi_dns_even.mif"
dwiextract: [100%] extracting volumes
mrmath: [100%] preloading data for "/tmp/mrtrix-tmp-aMg3oh.mif"
mrmath: [100%] computing mean along axis 3...

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:09 MST 2023:
COMMAND -->   mrconvert /tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.mif /tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz  
mrconvert: [100%] copying from "/tmp/6145_...228190/b0_meanMainPhase.mif" to "/tmp/6145_...190/b0_meanMainPhase.nii.gz"
mrconvert: [100%] compressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:09 MST 2023:
COMMAND -->   /opt/micapipe/functions/nifti_capture.py -img /tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz -out /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/QC/png/sub-00228190_ses-07_space-dwi_pe.png  

Check inputs:
  -img   : "['/tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz']"
   Number of img: "1"
  -out   : "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/QC/png/sub-00228190_ses-07_space-dwi_pe.png"
  -roi   : "False"
  -title :  ""

[INFO]... Creating single image png

[ INFO ]..... Extracting the rpe b0(s) 
            rpe dwgrad :    43
            rpe ndim   :    4
dwiextract: [100%] extracting volumes
mrmath: [100%] preloading data for "/tmp/mrtrix-tmp-qokx9U.mif"
mrmath: [100%] computing mean along axis 3...
mrmath: [100%] compressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_meanReversePhase.nii.gz"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:12 MST 2023:
COMMAND -->   mrconvert /tmp/6145_micapipe_proc-dwi_00228190/b0_meanReversePhase.nii.gz /tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz -coord 0 0:127 -coord 1 0:127 -coord 2 0:79 -force  
mrconvert: [WARNING] existing output files will be overwritten
mrconvert: [100%] uncompressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_meanReversePhase.nii.gz"
mrconvert: [100%] copying from "/tmp/6145_.../b0_meanReversePhase.nii.gz" to "/tmp/6145_...8190/b0_ReversePhase.nii.gz"
mrconvert: [100%] compressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz"

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:12 MST 2023:
COMMAND -->   /opt/micapipe/functions/nifti_capture.py -img /tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz -out /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/QC/png/sub-00228190_ses-07_space-dwi_rpe.png  

Check inputs:
  -img   : "['/tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz']"
   Number of img: "1"
  -out   : "/xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/QC/png/sub-00228190_ses-07_space-dwi_rpe.png"
  -roi   : "False"
  -title :  ""

[INFO]... Creating single image png

adamraikes @ r5u25n1.puma.hpc.arizona.edu Wed Mar  1 10:29:14 MST 2023:
COMMAND -->   mrcat /tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz /tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz /tmp/6145_micapipe_proc-dwi_00228190/b0_pair.mif -nthreads 8  
mrcat: [100%] uncompressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz"
mrcat: [100%] concatenating "/tmp/6145_micapipe_proc-dwi_00228190/b0_meanMainPhase.nii.gz"
mrcat: [100%] uncompressing image "/tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz"
mrcat: [100%] concatenating "/tmp/6145_micapipe_proc-dwi_00228190/b0_ReversePhase.nii.gz"

[ INFO ]..... dwifslpreproc parameters: 
        Shell values        :   1000
        DWI main dimensions :   128 128 80 43
        DWI rpe dimensions  :   128 128 80 43
        DWI to process dim  :   128 128 80 43
        pe_dir              :   j
        Readout Time        :   0.0455
        Options             :   -rpe_pair -align_seepi -se_epi /tmp/6145_micapipe_proc-dwi_00228190/b0_pair.mif
COMMAND --> dwifslpreproc /tmp/6145_micapipe_proc-dwi_00228190/dwi_dns_even.mif /xdisk/adamraikes/rush/derivatives/micapipe/micapipe/sub-00228190/ses-07/dwi/sub-00228190_ses-07_space-dwi_desc-dwi_preproc.mif -rpe_pair -align_seepi -se_epi /tmp/6145_micapipe_proc-dwi_00228190/b0_pair.mif -pe_dir j -readout_time 0.0455 -eddy_options " --data_is_shelled --slm=linear --repol" -nthreads 8 -nocleanup -scratch /tmp/6145_micapipe_proc-dwi_00228190 -force
dwifslpreproc: 
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: Generated scratch directory: /tmp/6145_micapipe_proc-dwi_00228190/dwifslpreproc-tmp-DCLMWE/
Command:  mrconvert /tmp/6145_micapipe_proc-dwi_00228190/dwi_dns_even.mif /tmp/6145_micapipe_proc-dwi_00228190/dwifslpreproc-tmp-DCLMWE/dwi.mif -json_export /tmp/6145_micapipe_proc-dwi_00228190/dwifslpreproc-tmp-DCLMWE/dwi.json
Command:  mrconvert /tmp/6145_micapipe_proc-dwi_00228190/b0_pair.mif /tmp/6145_micapipe_proc-dwi_00228190/dwifslpreproc-tmp-DCLMWE/se_epi.mif
dwifslpreproc: Changing to scratch directory (/tmp/6145_micapipe_proc-dwi_00228190/dwifslpreproc-tmp-DCLMWE/)
Command:  mrconvert dwi.mif dwi_first_bzero.mif -coord 3 0 -axes 0,1,2
dwifslpreproc: Balanced phase-encoding scheme detected in SE-EPI series; volume 0 will be removed and replaced with first b=0 from DWIs
Command:  mrconvert se_epi.mif - -coord 3 1 | mrcat dwi_first_bzero.mif - se_epi_firstdwibzero.mif -axis 3
Command:  mrinfo dwi.mif -export_grad_mrtrix grad.b
Command:  mrconvert se_epi_firstdwibzero.mif topup_in.nii -import_pe_table se_epi_manual_pe_scheme.txt -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
Command:  topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/opt/fsl-6.0.3/etc/flirtsch/b02b0.cnf --verbose
ajschadler12 commented 1 year ago

Hi @araikes: while I cannot speak to omitting the dwi_rpe option entirely, if you still wanted to use distortion correction for your dwi data, you can try using SynB0-DISCO to generate a synthetic, undistorted b0. You can then feed this synthetic, undistorted b0 to the dwi_rpe option.

rcruces commented 1 year ago

When there is no reverse phase encoding, the pipeline do not perform geometric distortion correction based on topup and eddy. One of the solutions would be what @ajschadler12 suggested. Currently we are not supporting geometric distortion correction when a rpe image is not included. However, the newest version might be able to improve the registrations due to its optimized registration engine. Please have a. look a it v0.2.0 Northern Flicker .

In future releases we are thinking about including options such as SynB0-DISCO but not for now