Summary of what happened:
Acquired two DTI sequences in opposite phase direction:
- b=1000 with 30 directions
- b=2000 with 60 directions
QSIprep was used to preprocess the scans. DTIFIT was used to create FA and RD maps which look good:
But when I run the QSIPrep NODDI recon, I get bad NDI images… it seems to give 0.99 values for voxels more superior, and normal values more inferior:
Whereas the OD looks good:
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -v ${fslicense}/license.txt:/opt/freesurfer/license.txt:ro -v ${BIDSdir}:/data:ro -v ${BIDSdir}/derivatives/qsiprep:/qsiprep-output:ro -v ${BIDSdir}/derivatives:/out -v ${workdir}:/scratch pennbbl/qsiprep:0.16.1 /data /out participant --recon-input /qsiprep-output --recon-spec amico_noddi --participant-label sub-${subid} --recon-only -w /scratch
Version:
0.16.1
Environment (Docker, Singularity, custom installation):
Docker, but I also ran the same analysis with the Python version of AMICO and got the same results
Data formatted according to a validatable standard? Please provide the output of the validator:
Yes, in BIDS format
Relevant log outputs (up to 20 lines):
No errors reported.
Screenshots / relevant information:
Here is the QSIPrep recon boilerplate image
Here is the pickle file:
{'version': '1.4.2', 'study_path': 'study', 'subject': 'subject', 'DATA_path': 'study/subject', 'OUTPUT_path': None, 'peaks_filename': None, 'doNormalizeSignal': True, 'doKeepb0Intact': False, 'doComputeNRMSE': False, 'doSaveCorrectedDWI': False, 'doMergeB0': False, 'doDebiasSignal': False, 'DWI-SNR': None, 'doDirectionalAverage': False, 'parallel_jobs': 7, 'parallel_backend': 'loky', 'verbose': 2, 'dwi_filename': '/scratch/qsirecon_wf/sub-Rett01_amico_noddi/sub_Rett01_space_T1w_desc_preproc_recon_wf/fit_noddi/recon_noddi/study/subject/sub-Rett01_space-T1w_desc-preproc_dwi.nii.gz', 'dim': (108, 129, 109), 'pixdim': (1.8, 1.8, 1.8), 'scheme_filename': '/scratch/qsirecon_wf/sub-Rett01_amico_noddi/sub_Rett01_space_T1w_desc_preproc_recon_wf/fit_noddi/recon_noddi/study/subject/sub-Rett01_space-T1w_desc-preproc_dwi.scheme', 'b0_thr': 50.0, 'ATOMS_path': 'study/kernels/NODDI', 'solver_params': {'mode': 2, 'pos': True, 'lambda1': 0.5, 'lambda2': 0.001}, 'lmax': 12, 'ndirs': 32761, 'fit_time': 5898.684504032135}