This panel shows the template T1-weighted image (if several T1w images were found), with contours delineating the detected brain mask and brain tissue segmentations.
Nonlinear mapping of the T1w image into MNI space. Hover on the panel with the mouse to transition between both spaces.
- A total of 2 distortion groups were included in the data data. Distortion group '0 1 0 0.071689' was represented by image 0 from sub-MS881355_ses-MS881355220321_run-1_dwi.nii.gz. Distortion group '0 -1 0 0.071689' was represented by image 0 from sub-MS881355_ses-MS881355220321_dir-AP_run-1_epi.nii.gz.
Effect of denoising on a low and high-b image.
Effect of bias correction on a low and high-b image. Bias field contour lines are drawn as an overlay.
The qform has been copied from sform.
b=0 template and final mask output. The t1 and signal intersection mask is blue, their xor is red and the entire mask is plotted in cyan.
Animation of the DWI sampling scheme. Each separate scan is its own color.
Results of performing susceptibility distortion correction (SDC) using b=0 images
antsRegistration was used to generate transformations from the b=0 reference image to the T1w-image.
Summary statistics are plotted.
/usr/local/miniconda/bin/qsiprep /n/nrg_l3/Lab/pipelines/SSBC/dwiqc/MS881355_220321 /n/nrg_l3/Lab/pipelines/SSBC/dwiqc/MS881355_220321/derivatives/dwiqc-qsiprep/sub-MS881355/ses-MS881355220321/sub-MS881355_ses-MS881355220321_run-1_dwi/qsiprep_output participant --output-resolution 1.0 --separate-all-dwis --eddy-config /n/nrg_l3/Lab/pipelines/SSBC/dwiqc/MS881355_220321/eddy_params_s2v_mbs.json --recon-spec reorient_fslstd --notrack --n_cpus 2 --mem_mb 40000 --fs-license-file /n/helmod/apps/centos7/Core/freesurfer/6.0.0-fasrc01/license.txt -w /n/holyscratch01/LABS/nrg/Lab/dasay/2532143We kindly ask to report results preprocessed with qsiprep using the following - boilerplate
- -Preprocessing was performed using QSIPrep 0.18.0, which is based on Nipype 1.8.6 (Gorgolewski et al. (2011); Gorgolewski et al. (2018); RRID:SCR_002502).
-The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) using N4BiasFieldCorrection (Tustison et al. 2010, ANTs 2.4.3), and used as an anatomical reference throughout the workflow. The anatomical reference image was reoriented into AC-PC alignment via a 6-DOF transform extracted from a full Affine registration to the MNI152NLin2009cAsym template. A full nonlinear registration to the template from AC-PC space was estimated via symmetric nonlinear registration (SyN) using antsRegistration. Brain extraction was performed on the T1w image using SynthStrip (Hoopes et al. 2022) and automated segmentation was performed using SynthSeg (Billot, Greve, et al. 2023, @synthseg2) from FreeSurfer version 7.3.1.
Any images with a b-value less than 100 s/mm^2 were treated as a b=0 image. MP-PCA denoising as implemented in MRtrix3’s dwidenoise(Veraart et al. 2016) was applied with a 5-voxel window. After MP-PCA, the mean intensity of the DWI series was adjusted so all the mean intensity of the b=0 images matched across eachseparate DWI scanning sequence. B1 field inhomogeneity was corrected using dwibiascorrect from MRtrix3 with the N4 algorithm (Tustison et al. 2010) after corrected images were resampled.
FSL (version 6.0.5.1:57b01774)’s eddy was used for head motion correction and Eddy current correction (Andersson and Sotiropoulos 2016). Eddy was configured with a q-space smoothing factor of 10, a total of 5 iterations, and 1000 voxels used to estimate hyperparameters. A quadratic first level model and a linear second level model were used to characterize Eddy current-related spatial distortion. q-space coordinates were forcefully assigned to shells. Field offset was attempted to be separated from subject movement. Shells were aligned post-eddy. Eddy’s outlier replacement was run (Andersson et al. 2016). Data were grouped by slice, only including values from slices determined to contain at least 250 intracerebral voxels. Groups deviating by more than 4 standard deviations from the prediction had their data replaced with imputed values. Slice-to-volume correction was estimated with temporal order 8, 5 iterations, trilinear interpolation and lambda=1.000 (Andersson et al. 2017). Data was collected with reversed phase-encode blips, resulting in pairs of images with distortions going in opposite directions. Here, b=0 reference images with reversed phase encoding directions were used along with an equal number of b=0 images extracted from the DWI scans. From these pairs the susceptibility-induced off-resonance field was estimated using a method similar to that described in (Andersson, Skare, and Ashburner 2003). The fieldmaps were ultimately incorporated into the Eddy current and head motion correction interpolation. Dynamic susceptibility distortion correction was applied with 10 iterations, lambda=10.00 and spline knot-spacing of 10.00mm (Andersson et al. 2018). Final interpolation was performed using the jac method.
Several confounding time-series were calculated based on the preprocessed DWI: framewise displacement (FD) using the implementation in Nipype (following the definitions by Power et al. 2014). The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. Slicewise cross correlation was also calculated. The DWI time-series were resampled to ACPC, generating a preprocessed DWI run in ACPC space with 1mm isotropic voxels.
-Many internal operations of QSIPrep use Nilearn 0.10.1 (Abraham et al. 2014, RRID:SCR_001362) and Dipy (Garyfallidis et al. 2014). For more details of the pipeline, see the section corresponding to workflows in QSIPrep’s documentation.
-Abraham, Alexandre, Fabian Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi, Alexandre Gramfort, Bertrand Thirion, and Gael Varoquaux. 2014. “Machine Learning for Neuroimaging with Scikit-Learn.” Frontiers in Neuroinformatics 8. https://doi.org/10.3389/fninf.2014.00014.
-Andersson, Jesper LR, Mark S Graham, Ivana Drobnjak, Hui Zhang, and Jon Campbell. 2018. “Susceptibility-Induced Distortion That Varies Due to Motion: Correction in Diffusion Mr Without Acquiring Additional Data.” Neuroimage 171. Elsevier: 277–95.
-Andersson, Jesper LR, Mark S Graham, Ivana Drobnjak, Hui Zhang, Nicola Filippini, and Matteo Bastiani. 2017. “Towards a Comprehensive Framework for Movement and Distortion Correction of Diffusion Mr Images: Within Volume Movement.” Neuroimage 152. Elsevier: 450–66.
-Andersson, Jesper LR, Mark S Graham, Enikő Zsoldos, and Stamatios N Sotiropoulos. 2016. “Incorporating Outlier Detection and Replacement into a Non-Parametric Framework for Movement and Distortion Correction of Diffusion Mr Images.” Neuroimage 141. Elsevier: 556–72.
-Andersson, Jesper LR, Stefan Skare, and John Ashburner. 2003. “How to Correct Susceptibility Distortions in Spin-Echo Echo-Planar Images: Application to Diffusion Tensor Imaging.” Neuroimage 20 (2). Elsevier: 870–88.
-Andersson, Jesper LR, and Stamatios N Sotiropoulos. 2016. “An Integrated Approach to Correction for Off-Resonance Effects and Subject Movement in Diffusion Mr Imaging.” Neuroimage 125. Elsevier: 1063–78.
-Billot, Benjamin, Douglas N Greve, Oula Puonti, Axel Thielscher, Koen Van Leemput, Bruce Fischl, Adrian V Dalca, Juan Eugenio Iglesias, and others. 2023. “SynthSeg: Segmentation of Brain Mri Scans of Any Contrast and Resolution Without Retraining.” Medical Image Analysis 86. Elsevier: 102789.
-Billot, Benjamin, Colin Magdamo, You Cheng, Steven E Arnold, Sudeshna Das, and Juan Eugenio Iglesias. 2023. “Robust Machine Learning Segmentation for Large-Scale Analysis of Heterogeneous Clinical Brain Mri Datasets.” Proceedings of the National Academy of Sciences 120 (9). National Acad Sciences: e2216399120.
-Garyfallidis, Eleftherios, Matthew Brett, Bagrat Amirbekian, Ariel Rokem, Stefan Van Der Walt, Maxime Descoteaux, and Ian Nimmo-Smith. 2014. “Dipy, a Library for the Analysis of Diffusion Mri Data.” Frontiers in Neuroinformatics 8. Frontiers: 8.
-Gorgolewski, K., C. D. Burns, C. Madison, D. Clark, Y. O. Halchenko, M. L. Waskom, and S. Ghosh. 2011. “Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python.” Frontiers in Neuroinformatics 5: 13. https://doi.org/10.3389/fninf.2011.00013.
-Gorgolewski, Krzysztof J., Oscar Esteban, Christopher J. Markiewicz, Erik Ziegler, David Gage Ellis, Michael Philipp Notter, Dorota Jarecka, et al. 2018. “Nipype.” Software. Zenodo. https://doi.org/10.5281/zenodo.596855.
-Hoopes, Andrew, Jocelyn S Mora, Adrian V Dalca, Bruce Fischl, and Malte Hoffmann. 2022. “SynthStrip: Skull-Stripping for Any Brain Image.” NeuroImage 260. Elsevier: 119474.
-Power, Jonathan D., Anish Mitra, Timothy O. Laumann, Abraham Z. Snyder, Bradley L. Schlaggar, and Steven E. Petersen. 2014. “Methods to Detect, Characterize, and Remove Motion Artifact in Resting State fMRI.” NeuroImage 84 (Supplement C): 320–41. https://doi.org/10.1016/j.neuroimage.2013.08.048.
-Tustison, N. J., B. B. Avants, P. A. Cook, Y. Zheng, A. Egan, P. A. Yushkevich, and J. C. Gee. 2010. “N4ITK: Improved N3 Bias Correction.” IEEE Transactions on Medical Imaging 29 (6): 1310–20. https://doi.org/10.1109/TMI.2010.2046908.
-Veraart, Jelle, Dmitry S Novikov, Daan Christiaens, Benjamin Ades-Aron, Jan Sijbers, and Els Fieremans. 2016. “Denoising of Diffusion Mri Using Random Matrix Theory.” NeuroImage 142. Elsevier: 394–406.
--Preprocessing was performed using *QSIPrep* 0.18.0, -which is based on *Nipype* 1.8.6 -(@nipype1; @nipype2; RRID:SCR_002502). - -Anatomical data preprocessing - -: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) -using `N4BiasFieldCorrection` [@n4, ANTs 2.4.3], -and used as an anatomical reference throughout the workflow. -The anatomical reference image was reoriented into AC-PC alignment via -a 6-DOF transform extracted from a full Affine registration to the -MNI152NLin2009cAsym template. A full nonlinear registration to the template from AC-PC space was -estimated via symmetric nonlinear registration (SyN) using antsRegistration. Brain extraction was performed on the T1w image using -SynthStrip [@synthstrip] and automated segmentation was -performed using SynthSeg [@synthseg1, @synthseg2] from -FreeSurfer version 7.3.1. - -Diffusion data preprocessing - -: Any images with a b-value less than 100 s/mm^2 were treated as a *b*=0 image. MP-PCA denoising as implemented in MRtrix3's `dwidenoise`[@dwidenoise1] was applied with a 5-voxel window. After MP-PCA, the mean intensity of the DWI series was adjusted so all the mean intensity of the b=0 images matched across eachseparate DWI scanning sequence. B1 field inhomogeneity was corrected using `dwibiascorrect` from MRtrix3 with the N4 algorithm [@n4] after corrected images were resampled. - -FSL (version 6.0.5.1:57b01774)'s eddy was used for head motion correction and Eddy current correction [@anderssoneddy]. Eddy was configured with a $q$-space smoothing factor of 10, a total of 5 iterations, and 1000 voxels used to estimate hyperparameters. A quadratic first level model and a linear second level model were used to characterize Eddy current-related spatial distortion. $q$-space coordinates were forcefully assigned to shells. Field offset was attempted to be separated from subject movement. Shells were aligned post-eddy. Eddy's outlier replacement was run [@eddyrepol]. Data were grouped by slice, only including values from slices determined to contain at least 250 intracerebral voxels. Groups deviating by more than 4 standard deviations from the prediction had their data replaced with imputed values. Slice-to-volume correction was estimated with temporal order 8, 5 iterations, trilinear interpolation and lambda=1.000 [@eddys2v]. Data was collected with reversed phase-encode blips, resulting in pairs of images with distortions going in opposite directions. Here, b=0 reference images with reversed phase encoding directions were used along with an equal number of b=0 images extracted from the DWI scans. From these pairs the susceptibility-induced off-resonance field was estimated using a method similar to that described in [@topup]. The fieldmaps were ultimately incorporated into the Eddy current and head motion correction interpolation. Dynamic susceptibility distortion correction was applied with 10 iterations, lambda=10.00 and spline knot-spacing of 10.00mm [@eddysus]. Final interpolation was performed using the `jac` method. - -Several confounding time-series were calculated based on the -preprocessed DWI: framewise displacement (FD) using the -implementation in *Nipype* [following the definitions by @power_fd_dvars]. -The head-motion estimates calculated in the correction step were also -placed within the corresponding confounds file. Slicewise cross correlation -was also calculated. -The DWI time-series were resampled to ACPC, -generating a *preprocessed DWI run in ACPC space* with 1mm isotropic voxels. - - -Many internal operations of *QSIPrep* use -*Nilearn* 0.10.1 [@nilearn, RRID:SCR_001362] and -*Dipy* [@dipy]. -For more details of the pipeline, see [the section corresponding -to workflows in *QSIPrep*'s documentation](https://qsiprep.readthedocs.io/en/latest/workflows.html "QSIPrep's documentation"). - - -### References - --
Preprocessing was performed using \emph{QSIPrep} 0.18.0, which is based
-on \emph{Nipype} 1.8.6 (\citet{nipype1}; \citet{nipype2};
-RRID:SCR\_002502).
-
-\begin{description}
-\item[Anatomical data preprocessing]
-The T1-weighted (T1w) image was corrected for intensity non-uniformity
-(INU) using \texttt{N4BiasFieldCorrection} \citep[ANTs 2.4.3]{n4}, and
-used as an anatomical reference throughout the workflow. The anatomical
-reference image was reoriented into AC-PC alignment via a 6-DOF
-transform extracted from a full Affine registration to the
-MNI152NLin2009cAsym template. A full nonlinear registration to the
-template from AC-PC space was estimated via symmetric nonlinear
-registration (SyN) using antsRegistration. Brain extraction was
-performed on the T1w image using SynthStrip \citep{synthstrip} and
-automated segmentation was performed using SynthSeg
-\citep[\citet{synthseg2}]{synthseg1} from FreeSurfer version 7.3.1.
-\item[Diffusion data preprocessing]
-Any images with a b-value less than 100 s/mm\^{}2 were treated as a
-\emph{b}=0 image. MP-PCA denoising as implemented in MRtrix3's
-\texttt{dwidenoise}\citep{dwidenoise1} was applied with a 5-voxel
-window. After MP-PCA, the mean intensity of the DWI series was adjusted
-so all the mean intensity of the b=0 images matched across eachseparate
-DWI scanning sequence. B1 field inhomogeneity was corrected using
-\texttt{dwibiascorrect} from MRtrix3 with the N4 algorithm \citep{n4}
-after corrected images were resampled.
-\end{description}
-
-FSL (version 6.0.5.1:57b01774)'s eddy was used for head motion
-correction and Eddy current correction \citep{anderssoneddy}. Eddy was
-configured with a \(q\)-space smoothing factor of 10, a total of 5
-iterations, and 1000 voxels used to estimate hyperparameters. A
-quadratic first level model and a linear second level model were used to
-characterize Eddy current-related spatial distortion. \(q\)-space
-coordinates were forcefully assigned to shells. Field offset was
-attempted to be separated from subject movement. Shells were aligned
-post-eddy. Eddy's outlier replacement was run \citep{eddyrepol}. Data
-were grouped by slice, only including values from slices determined to
-contain at least 250 intracerebral voxels. Groups deviating by more than
-4 standard deviations from the prediction had their data replaced with
-imputed values. Slice-to-volume correction was estimated with temporal
-order 8, 5 iterations, trilinear interpolation and lambda=1.000
-\citep{eddys2v}. Data was collected with reversed phase-encode blips,
-resulting in pairs of images with distortions going in opposite
-directions. Here, b=0 reference images with reversed phase encoding
-directions were used along with an equal number of b=0 images extracted
-from the DWI scans. From these pairs the susceptibility-induced
-off-resonance field was estimated using a method similar to that
-described in \citep{topup}. The fieldmaps were ultimately incorporated
-into the Eddy current and head motion correction interpolation. Dynamic
-susceptibility distortion correction was applied with 10 iterations,
-lambda=10.00 and spline knot-spacing of 10.00mm \citep{eddysus}. Final
-interpolation was performed using the \texttt{jac} method.
-
-Several confounding time-series were calculated based on the
-preprocessed DWI: framewise displacement (FD) using the implementation
-in \emph{Nipype} \citep[following the definitions by][]{power_fd_dvars}.
-The head-motion estimates calculated in the correction step were also
-placed within the corresponding confounds file. Slicewise cross
-correlation was also calculated. The DWI time-series were resampled to
-ACPC, generating a \emph{preprocessed DWI run in ACPC space} with 1mm
-isotropic voxels.
-
-Many internal operations of \emph{QSIPrep} use \emph{Nilearn} 0.10.1
-\citep[RRID:SCR\_001362]{nilearn} and \emph{Dipy} \citep{dipy}. For more
-details of the pipeline, see
-\href{https://qsiprep.readthedocs.io/en/latest/workflows.html}{the
-section corresponding to workflows in \emph{QSIPrep}'s documentation}.
-
-\hypertarget{references}{%
-\subsubsection{References}\label{references}}
-
-\bibliography{/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/data/boilerplate.bib}
-@article{fmriprep1,
- author = {Esteban, Oscar and Markiewicz, Christopher and Blair, Ross W and Moodie, Craig and Isik, Ayse Ilkay and Erramuzpe Aliaga, Asier and Kent, James and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit and Wright, Jessey and Durnez, Joke and Poldrack, Russell and Gorgolewski, Krzysztof Jacek},
- title = {fmriprep: a robust preprocessing pipeline for functional {MRI}},
- year = {2018},
- doi = {10.1101/306951},
- journal = {bioRxiv}
-}
-
-@article{fmriprep2,
- author = {Esteban, Oscar and Blair, Ross and Markiewicz, Christopher J. and Berleant, Shoshana L. and Moodie, Craig and Ma, Feilong and Isik, Ayse Ilkay and Erramuzpe, Asier and Kent, James D. andGoncalves, Mathias and DuPre, Elizabeth and Sitek, Kevin R. and Gomez, Daniel E. P. and Lurie, Daniel J. and Ye, Zhifang and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
- title = {fmriprep},
- year = 2018,
- doi = {10.5281/zenodo.852659},
- publisher = {Zenodo},
- journal = {Software}
-}
-
-@article{dipy,
- title={Dipy, a library for the analysis of diffusion MRI data},
- author={Garyfallidis, Eleftherios and Brett, Matthew and Amirbekian, Bagrat and Rokem, Ariel and Van Der Walt, Stefan and Descoteaux, Maxime and Nimmo-Smith, Ian},
- journal={Frontiers in neuroinformatics},
- volume={8},
- pages={8},
- year={2014},
- publisher={Frontiers}
-}
-
-
-@article{pyafq,
- title = {Evaluating the reliability of human brain white matter tractometry},
- author = {Kruper, J., Yeatman, J.D., Richie-Halford, A., Bloom, D., Grotheer, M., Caffarra, S., Kiar, G., Karipidis, I.I., Roy, E., Chandio, B.Q., Garyfallidis, E., & Rokem, A.},
- journal = {Aperture Neuro},
- volume = {1},
- pages = {1-25},
- year = {2021},
-}
-
-@article{pyafq2,
- title = {Tract profiles of White Matter Properties: Automating fiber-tract quantification},
- volume = {7},
- doi = {10.1371/journal.pone.0049790},
- number = {11},
- journal = {PLoS ONE},
- author = {Yeatman, Jason D. and Dougherty, Robert F. and Myall, Nathaniel J. and Wandell, Brian A. and Feldman, Heidi M.},
- year = {2012}
-}
-
-@article{nipype1,
- author = {Gorgolewski, K. and Burns, C. D. and Madison, C. and Clark, D. and Halchenko, Y. O. and Waskom, M. L. and Ghosh, S.},
- doi = {10.3389/fninf.2011.00013},
- journal = {Frontiers in Neuroinformatics},
- pages = 13,
- shorttitle = {Nipype},
- title = {Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python},
- volume = 5,
- year = 2011
-}
-
-@article{nipype2,
- author = {Gorgolewski, Krzysztof J. and Esteban, Oscar and Markiewicz, Christopher J. and Ziegler, Erik and Ellis, David Gage and Notter, Michael Philipp and Jarecka, Dorota and Johnson, Hans and Burns, Christopher and Manhães-Savio, Alexandre and Hamalainen, Carlo and Yvernault, Benjamin and Salo, Taylor and Jordan, Kesshi and Goncalves, Mathias and Waskom, Michael and Clark, Daniel and Wong, Jason and Loney, Fred and Modat, Marc and Dewey, Blake E and Madison, Cindee and Visconti di Oleggio Castello, Matteo and Clark, Michael G. and Dayan, Michael and Clark, Dav and Keshavan, Anisha and Pinsard, Basile and Gramfort, Alexandre and Berleant, Shoshana and Nielson, Dylan M. and Bougacha, Salma and Varoquaux, Gael and Cipollini, Ben and Markello, Ross and Rokem, Ariel and Moloney, Brendan and Halchenko, Yaroslav O. and Wassermann , Demian and Hanke, Michael and Horea, Christian and Kaczmarzyk, Jakub and Gilles de Hollander and DuPre, Elizabeth and Gillman, Ashley and Mordom, David and Buchanan, Colin and Tungaraza, Rosalia and Pauli, Wolfgang M. and Iqbal, Shariq and Sikka, Sharad and Mancini, Matteo and Schwartz, Yannick and Malone, Ian B. and Dubois, Mathieu and Frohlich, Caroline and Welch, David and Forbes, Jessica and Kent, James and Watanabe, Aimi and Cumba, Chad and Huntenburg, Julia M. and Kastman, Erik and Nichols, B. Nolan and Eshaghi, Arman and Ginsburg, Daniel and Schaefer, Alexander and Acland, Benjamin and Giavasis, Steven and Kleesiek, Jens and Erickson, Drew and Küttner, René and Haselgrove, Christian and Correa, Carlos and Ghayoor, Ali and Liem, Franz and Millman, Jarrod and Haehn, Daniel and Lai, Jeff and Zhou, Dale and Blair, Ross and Glatard, Tristan and Renfro, Mandy and Liu, Siqi and Kahn, Ari E. and Pérez-García, Fernando and Triplett, William and Lampe, Leonie and Stadler, Jörg and Kong, Xiang-Zhen and Hallquist, Michael and Chetverikov, Andrey and Salvatore, John and Park, Anne and Poldrack, Russell and Craddock, R. Cameron and Inati, Souheil and Hinds, Oliver and Cooper, Gavin and Perkins, L. Nathan and Marina, Ana and Mattfeld, Aaron and Noel, Maxime and Lukas Snoek and Matsubara, K and Cheung, Brian and Rothmei, Simon and Urchs, Sebastian and Durnez, Joke and Mertz, Fred and Geisler, Daniel and Floren, Andrew and Gerhard, Stephan and Sharp, Paul and Molina-Romero, Miguel and Weinstein, Alejandro and Broderick, William and Saase, Victor and Andberg, Sami Kristian and Harms, Robbert and Schlamp, Kai and Arias, Jaime and Papadopoulos Orfanos, Dimitri and Tarbert, Claire and Tambini, Arielle and De La Vega, Alejandro and Nickson, Thomas and Brett, Matthew and Falkiewicz, Marcel and Podranski, Kornelius and Linkersdörfer, Janosch and Flandin, Guillaume and Ort, Eduard and Shachnev, Dmitry and McNamee, Daniel and Davison, Andrew and Varada, Jan and Schwabacher, Isaac and Pellman, John and Perez-Guevara, Martin and Khanuja, Ranjeet and Pannetier, Nicolas and McDermottroe, Conor and Ghosh, Satrajit},
- title = {Nipype},
- year = 2018,
- doi = {10.5281/zenodo.596855},
- publisher = {Zenodo},
- journal = {Software}
-}
-
-@article{n4,
- author = {Tustison, N. J. and Avants, B. B. and Cook, P. A. and Zheng, Y. and Egan, A. and Yushkevich, P. A. and Gee, J. C.},
- doi = {10.1109/TMI.2010.2046908},
- issn = {0278-0062},
- journal = {IEEE Transactions on Medical Imaging},
- number = 6,
- pages = {1310-1320},
- shorttitle = {N4ITK},
- title = {N4ITK: Improved N3 Bias Correction},
- volume = 29,
- year = 2010
-}
-
-@article{fs_reconall,
- author = {Dale, Anders M. and Fischl, Bruce and Sereno, Martin I.},
- doi = {10.1006/nimg.1998.0395},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 2,
- pages = {179-194},
- shorttitle = {Cortical Surface-Based Analysis},
- title = {Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811998903950},
- volume = 9,
- year = 1999
-}
-
-
-
-@article{mindboggle,
- author = {Klein, Arno and Ghosh, Satrajit S. and Bao, Forrest S. and Giard, Joachim and Häme, Yrjö and Stavsky, Eliezer and Lee, Noah and Rossa, Brian and Reuter, Martin and Neto, Elias Chaibub and Keshavan, Anisha},
- doi = {10.1371/journal.pcbi.1005350},
- issn = {1553-7358},
- journal = {PLOS Computational Biology},
- number = 2,
- pages = {e1005350},
- title = {Mindboggling morphometry of human brains},
- url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350},
- volume = 13,
- year = 2017
-}
-
-@article{mni,
- author = {Fonov, VS and Evans, AC and McKinstry, RC and Almli, CR and Collins, DL},
- doi = {10.1016/S1053-8119(09)70884-5},
- issn = {1053-8119},
- journal = {NeuroImage},
- pages = {S102},
- series = {Organization for Human Brain Mapping 2009 Annual Meeting},
- title = {Unbiased nonlinear average age-appropriate brain templates from birth to adulthood},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811909708845},
- volume = {47, Supplement 1},
- year = 2009
-}
-
-@article{ants,
- author = {Avants, B.B. and Epstein, C.L. and Grossman, M. and Gee, J.C.},
- doi = {10.1016/j.media.2007.06.004},
- issn = {1361-8415},
- journal = {Medical Image Analysis},
- number = 1,
- pages = {26-41},
- shorttitle = {Symmetric diffeomorphic image registration with cross-correlation},
- title = {Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain},
- url = {http://www.sciencedirect.com/science/article/pii/S1361841507000606},
- volume = 12,
- year = 2008
-}
-
-@article{fsl_fast,
- author = {Zhang, Y. and Brady, M. and Smith, S.},
- doi = {10.1109/42.906424},
- issn = {0278-0062},
- journal = {IEEE Transactions on Medical Imaging},
- number = 1,
- pages = {45-57},
- title = {Segmentation of brain {MR} images through a hidden Markov random field model and the expectation-maximization algorithm},
- volume = 20,
- year = 2001
-}
-
-@article{fieldmapless1,
- author = {Wang, Sijia and Peterson, Daniel J. and Gatenby, J. C. and Li, Wenbin and Grabowski, Thomas J. and Madhyastha, Tara M.},
- doi = {10.3389/fninf.2017.00017},
- issn = {1662-5196},
- journal = {Frontiers in Neuroinformatics},
- language = {English},
- title = {Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion {MRI}},
- url = {http://journal.frontiersin.org/article/10.3389/fninf.2017.00017/full},
- volume = 11,
- year = 2017
-}
-
-@phdthesis{fieldmapless2,
- address = {Berlin},
- author = {Huntenburg, Julia M.},
- language = {eng},
- school = {Freie Universität},
- title = {Evaluating nonlinear coregistration of {BOLD} {EPI} and T1w images},
- type = {Master's Thesis},
- url = {http://hdl.handle.net/11858/00-001M-0000-002B-1CB5-A},
- year = 2014
-}
-
-@article{fieldmapless3,
- author = {Treiber, Jeffrey Mark and White, Nathan S. and Steed, Tyler Christian and Bartsch, Hauke and Holland, Dominic and Farid, Nikdokht and McDonald, Carrie R. and Carter, Bob S. and Dale, Anders Martin and Chen, Clark C.},
- doi = {10.1371/journal.pone.0152472},
- issn = {1932-6203},
- journal = {PLOS ONE},
- number = 3,
- pages = {e0152472},
- title = {Characterization and Correction of Geometric Distortions in 814 Diffusion Weighted Images},
- url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152472},
- volume = 11,
- year = 2016
-}
-
-@article{flirt,
- title = {A global optimisation method for robust affine registration of brain images},
- volume = {5},
- issn = {1361-8415},
- url = {http://www.sciencedirect.com/science/article/pii/S1361841501000366},
- doi = {10.1016/S1361-8415(01)00036-6},
- number = {2},
- urldate = {2018-07-27},
- journal = {Medical Image Analysis},
- author = {Jenkinson, Mark and Smith, Stephen},
- year = {2001},
- keywords = {Affine transformation, flirt, fsl, Global optimisation, Multi-resolution search, Multimodal registration, Robustness},
- pages = {143--156}
-}
-
-@article{mcflirt,
- author = {Jenkinson, Mark and Bannister, Peter and Brady, Michael and Smith, Stephen},
- doi = {10.1006/nimg.2002.1132},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 2,
- pages = {825-841},
- title = {Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811902911328},
- volume = 17,
- year = 2002
-}
-
-@article{bbr,
- author = {Greve, Douglas N and Fischl, Bruce},
- doi = {10.1016/j.neuroimage.2009.06.060},
- issn = {1095-9572},
- journal = {NeuroImage},
- number = 1,
- pages = {63-72},
- title = {Accurate and robust brain image alignment using boundary-based registration},
- volume = 48,
- year = 2009
-}
-
-@article{aroma,
- author = {Pruim, Raimon H. R. and Mennes, Maarten and van Rooij, Daan and Llera, Alberto and Buitelaar, Jan K. and Beckmann, Christian F.},
- doi = {10.1016/j.neuroimage.2015.02.064},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = {Supplement C},
- pages = {267-277},
- shorttitle = {ICA-AROMA},
- title = {ICA-{AROMA}: A robust {ICA}-based strategy for removing motion artifacts from fMRI data},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811915001822},
- volume = 112,
- year = 2015
-}
-
-@article{power_fd_dvars,
- author = {Power, Jonathan D. and Mitra, Anish and Laumann, Timothy O. and Snyder, Abraham Z. and Schlaggar, Bradley L. and Petersen, Steven E.},
- doi = {10.1016/j.neuroimage.2013.08.048},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = {Supplement C},
- pages = {320-341},
- title = {Methods to detect, characterize, and remove motion artifact in resting state fMRI},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811913009117},
- volume = 84,
- year = 2014
-}
-
-@article{nilearn,
- author = {Abraham, Alexandre and Pedregosa, Fabian and Eickenberg, Michael and Gervais, Philippe and Mueller, Andreas and Kossaifi, Jean and Gramfort, Alexandre and Thirion, Bertrand and Varoquaux, Gael},
- doi = {10.3389/fninf.2014.00014},
- issn = {1662-5196},
- journal = {Frontiers in Neuroinformatics},
- language = {English},
- title = {Machine learning for neuroimaging with scikit-learn},
- url = {https://www.frontiersin.org/articles/10.3389/fninf.2014.00014/full},
- volume = 8,
- year = 2014
-}
-
-@article{lanczos,
- author = {Lanczos, C.},
- doi = {10.1137/0701007},
- issn = {0887-459X},
- journal = {Journal of the Society for Industrial and Applied Mathematics Series B Numerical Analysis},
- number = 1,
- pages = {76-85},
- title = {Evaluation of Noisy Data},
- url = {http://epubs.siam.org/doi/10.1137/0701007},
- volume = 1,
- year = 1964
-}
-
-@article{compcor,
- author = {Behzadi, Yashar and Restom, Khaled and Liau, Joy and Liu, Thomas T.},
- doi = {10.1016/j.neuroimage.2007.04.042},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 1,
- pages = {90-101},
- title = {A component based noise correction method ({CompCor}) for {BOLD} and perfusion based fMRI},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811907003837},
- volume = 37,
- year = 2007
-}
-
-@article{hcppipelines,
- author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark},
- doi = {10.1016/j.neuroimage.2013.04.127},
- issn = {1053-8119},
- journal = {NeuroImage},
- pages = {105-124},
- series = {Mapping the Connectome},
- title = {The minimal preprocessing pipelines for the Human Connectome Project},
- url = {http://www.sciencedirect.com/science/article/pii/S1053811913005053},
- volume = 80,
- year = 2013
-}
-
-@article{fs_template,
- author = {Reuter, Martin and Rosas, Herminia Diana and Fischl, Bruce},
- doi = {10.1016/j.neuroimage.2010.07.020},
- journal = {NeuroImage},
- number = 4,
- pages = {1181-1196},
- title = {Highly accurate inverse consistent registration: A robust approach},
- volume = 53,
- year = 2010
-}
-
-@article{afni,
- author = {Cox, Robert W. and Hyde, James S.},
- doi = {10.1002/(SICI)1099-1492(199706/08)10:4/5<171::AID-NBM453>3.0.CO;2-L},
- journal = {NMR in Biomedicine},
- number = {4-5},
- pages = {171-178},
- title = {Software tools for analysis and visualization of fMRI data},
- volume = 10,
- year = 1997
-}
-
-@article{posse_t2s,
- author = {Posse, Stefan and Wiese, Stefan and Gembris, Daniel and Mathiak, Klaus and Kessler, Christoph and Grosse-Ruyken, Maria-Liisa and Elghahwagi, Barbara and Richards, Todd and Dager, Stephen R. and Kiselev, Valerij G.},
- doi = {10.1002/(SICI)1522-2594(199907)42:1<87::AID-MRM13>3.0.CO;2-O},
- journal = {Magnetic Resonance in Medicine},
- number = 1,
- pages = {87-97},
- title = {Enhancement of {BOLD}-contrast sensitivity by single-shot multi-echo functional {MR} imaging},
- volume = 42,
- year = 1999
-}
-
-@article{dwidenoise1,
- title={Denoising of diffusion MRI using random matrix theory},
- author={Veraart, Jelle and Novikov, Dmitry S and Christiaens, Daan and Ades-Aron, Benjamin and Sijbers, Jan and Fieremans, Els},
- journal={NeuroImage},
- volume={142},
- pages={394--406},
- year={2016},
- publisher={Elsevier}
-}
-
-@article{dwidenoise2,
- title={Diffusion MRI noise mapping using random matrix theory},
- author={Veraart, Jelle and Fieremans, Els and Novikov, Dmitry S},
- journal={Magnetic resonance in medicine},
- volume={76},
- number={5},
- pages={1582--1593},
- year={2016},
- publisher={Wiley Online Library}
-}
-
-@article{merlet3dshore,
- title={Continuous diffusion signal, EAP and ODF estimation via compressive sensing in diffusion MRI},
- author={Merlet, Sylvain L and Deriche, Rachid},
- journal={Medical image analysis},
- volume={17},
- number={5},
- pages={556--572},
- year={2013},
- publisher={Elsevier}
-}
-
-@article{pncprocessing,
- title={Neuroimaging of the Philadelphia neurodevelopmental cohort},
- author={Satterthwaite, Theodore D and Elliott, Mark A and Ruparel, Kosha and Loughead, James and Prabhakaran, Karthik and Calkins, Monica E and Hopson, Ryan and Jackson, Chad and Keefe, Jack and Riley, Marisa and others},
- journal={Neuroimage},
- volume={86},
- pages={544--553},
- year={2014},
- publisher={Elsevier}
-}
-
-@inproceedings{dhollander2019response,
- title={Improved white matter response function estimation for 3-tissue constrained spherical deconvolution},
- author={Dhollander, T and Mito, R and Raffelt, D and Connelly, A},
- booktitle={Proc. Intl. Soc. Mag. Reson. Med},
- pages={555},
- year={2019}
-}
-
-@inproceedings{dhollander2016unsupervised,
- title={Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image},
- author={Dhollander, Thijs and Raffelt, David and Connelly, Alan},
- booktitle={ISMRM Workshop on Breaking the Barriers of Diffusion MRI},
- volume={5},
- pages={5},
- year={2016}
-}
-
-@article{msmt5tt,
- title={Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data},
- author={Jeurissen, Ben and Tournier, Jacques-Donald and Dhollander, Thijs and Connelly, Alan and Sijbers, Jan},
- journal={NeuroImage},
- volume={103},
- pages={411--426},
- year={2014},
- publisher={Elsevier}
-}
-
-@article{mrtrix3,
- title = {MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation},
- author = {J-Donald and Smith, Robert and Raffelt, David and Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and Christiaens, Daan and Jeurissen, Ben and Yeh, Chun-Hung and Connelly, Alan"},
- journal = {NeuroImage},
- volume = {202},
- pages = {116137},
- year = {2019},
- issn={1053-8119},
-}
-
-@article{originalcsd,
- title={Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution},
- author={Tournier, J-Donald and Calamante, Fernando and Gadian, David G and Connelly, Alan},
- journal={NeuroImage},
- volume={23},
- number={3},
- pages={1176--1185},
- year={2004},
- publisher={Elsevier}
-}
-
-@article{tournier2007robust,
- title={Robust determination of the fibre orientation distribution in diffusion MRI: non-negativity constrained super-resolved spherical deconvolution},
- author={Tournier, J-Donald and Calamante, Fernando and Connelly, Alan},
- journal={Neuroimage},
- volume={35},
- number={4},
- pages={1459--1472},
- year={2007},
- publisher={Elsevier}
-}
-
-@article{tournier2008csd,
- title={Resolving crossing fibres using constrained spherical deconvolution: validation using diffusion-weighted imaging phantom data},
- author={Tournier, J-Donald and Yeh, Chun-Hung and Calamante, Fernando and Cho, Kuan-Hung and Connelly, Alan and Lin, Ching-Po},
- journal={Neuroimage},
- volume={42},
- number={2},
- pages={617--625},
- year={2008},
- publisher={Elsevier}
-}
-
-@inproceedings{mtnormalize,
- title={Bias field correction and intensity normalisation for quantitative analysis of apparent fibre density},
- author={Raffelt, David and Dhollander, Thijs and Tournier, J-Donald and Tabbara, Rami and Smith, Robert E and Pierre, Eric and Connelly, Alan},
- booktitle={Proc. Intl. Soc. Mag. Reson. Med},
- volume={25},
- pages={3541},
- year={2017}
-}
-
-@article{yeh2010gqi,
- title={Generalized $q$-sampling imaging},
- author={Yeh, Fang-Cheng and Wedeen, Van Jay and Tseng, Wen-Yih Isaac},
- journal={IEEE transactions on medical imaging},
- volume={29},
- number={9},
- pages={1626--1635},
- year={2010},
- publisher={IEEE}
-}
-
-@article{anderssoneddy,
- title={An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging},
- author={Andersson, Jesper LR and Sotiropoulos, Stamatios N},
- journal={Neuroimage},
- volume={125},
- pages={1063--1078},
- year={2016},
- publisher={Elsevier}
-}
-
-@article{eddyrepol,
- title={Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images},
- author={Andersson, Jesper LR and Graham, Mark S and Zsoldos, Enik{\H{o}} and Sotiropoulos, Stamatios N},
- journal={Neuroimage},
- volume={141},
- pages={556--572},
- year={2016},
- publisher={Elsevier}
-}
-
-@article{fsllsr,
- title={How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging},
- author={Andersson, Jesper LR and Skare, Stefan and Ashburner, John},
- journal={Neuroimage},
- volume={20},
- number={2},
- pages={870--888},
- year={2003},
- publisher={Elsevier}
-}
-
-
-@article{eddysus,
- title={Susceptibility-induced distortion that varies due to motion: correction in diffusion MR without acquiring additional data},
- author={Andersson, Jesper LR and Graham, Mark S and Drobnjak, Ivana and Zhang, Hui and Campbell, Jon},
- journal={Neuroimage},
- volume={171},
- pages={277--295},
- year={2018},
- publisher={Elsevier}
-}
-
-@article{eddys2v,
- title={Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement},
- author={Andersson, Jesper LR and Graham, Mark S and Drobnjak, Ivana and Zhang, Hui and Filippini, Nicola and Bastiani, Matteo},
- journal={Neuroimage},
- volume={152},
- pages={450--466},
- year={2017},
- publisher={Elsevier}
-}
-
-@article{topup,
- title={How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging},
- author={Andersson, Jesper LR and Skare, Stefan and Ashburner, John},
- journal={Neuroimage},
- volume={20},
- number={2},
- pages={870--888},
- year={2003},
- publisher={Elsevier}
-}
-
-@article{mrdegibbs,
- title={Gibbs-ringing artifact removal based on local subvoxel-shifts},
- author={Kellner, Elias and Dhital, Bibek and Kiselev, Valerij G and Reisert, Marco},
- journal={Magnetic resonance in medicine},
- volume={76},
- number={5},
- pages={1574--1581},
- year={2016},
- publisher={Wiley Online Library}
-}
-
-@article{patch2self,
- title={Patch2Self: Denoising Diffusion MRI with Self-Supervised Learning},
- author={Fadnavis, Shreyas and Batson, Joshua and Garyfallidis, Eleftherios},
- journal={Advances in Neural Information Processing Systems},
- volume={33},
- year={2020}
-}
-
-@article{noddi,
- title={NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain},
- author={Zhang, Hui and Schneider, Torben and Wheeler-Kingshott, Claudia A and Alexander, Daniel C},
- journal={Neuroimage},
- volume={61},
- number={4},
- pages={1000--1016},
- year={2012},
- publisher={Elsevier}
-}
-
-@article{amico,
- title={Accelerated microstructure imaging via convex optimization (AMICO) from diffusion MRI data},
- author={Daducci, Alessandro and Canales-Rodr{\'\i}guez, Erick J and Zhang, Hui and Dyrby, Tim B and Alexander, Daniel C and Thiran, Jean-Philippe},
- journal={NeuroImage},
- volume={105},
- pages={32--44},
- year={2015},
- publisher={Elsevier}
-}
-
-@article{drbuddi,
- title={DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions},
- author={Irfanoglu, M Okan and Modi, Pooja and Nayak, Amritha and Hutchinson, Elizabeth B and Sarlls, Joelle and Pierpaoli, Carlo},
- journal={Neuroimage},
- volume={106},
- pages={284--299},
- year={2015},
- publisher={Elsevier}
-}
-
-@inproceedings{tortoisev3,
- title={TORTOISE v3: Improvements and new features of the NIH diffusion MRI processing pipeline},
- author={Irfanoglu, Mustafa Okan and Nayak, Amritha and Jenkins, Jeffrey and Pierpaoli, Carlo},
- booktitle={Program and proceedings of the ISMRM 25th annual meeting and exhibition, Honolulu, HI, USA},
- year={2017}
-}
-
-@article{pfgibbs,
- title={Removal of partial Fourier-induced Gibbs (RPG) ringing artifacts in MRI},
- author={Lee, Hong-Hsi and Novikov, Dmitry S and Fieremans, Els},
- journal={Magnetic Resonance in Medicine},
- volume={86},
- number={5},
- pages={2733--2750},
- year={2021},
- publisher={Wiley Online Library}
-}
-
-@article{synthstrip,
- title={SynthStrip: skull-stripping for any brain image},
- author={Hoopes, Andrew and Mora, Jocelyn S and Dalca, Adrian V and Fischl, Bruce and Hoffmann, Malte},
- journal={NeuroImage},
- volume={260},
- pages={119474},
- year={2022},
- publisher={Elsevier}
-}
-
-@article{synthseg1,
- title={SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining},
- author={Billot, Benjamin and Greve, Douglas N and Puonti, Oula and Thielscher, Axel and Van Leemput, Koen and Fischl, Bruce and Dalca, Adrian V and Iglesias, Juan Eugenio and others},
- journal={Medical image analysis},
- volume={86},
- pages={102789},
- year={2023},
- publisher={Elsevier}
-}
-
-@article{synthseg2,
- title={Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets},
- author={Billot, Benjamin and Magdamo, Colin and Cheng, You and Arnold, Steven E and Das, Sudeshna and Iglesias, Juan Eugenio},
- journal={Proceedings of the National Academy of Sciences},
- volume={120},
- number={9},
- pages={e2216399120},
- year={2023},
- publisher={National Acad Sciences}
-}
-
-@article{yeh2013deterministic,
- title={Deterministic diffusion fiber tracking improved by quantitative anisotropy},
- author={Yeh, Fang-Cheng and Verstynen, Timothy D and Wang, Yibao and Fern{\'a}ndez-Miranda, Juan C and Tseng, Wen-Yih Isaac},
- journal={PloS one},
- volume={8},
- number={11},
- pages={e80713},
- year={2013},
- publisher={Public Library of Science San Francisco, USA}
-}
-
-@article{autotrack,
- title={Shape analysis of the human association pathways},
- author={Yeh, Fang-Cheng},
- journal={Neuroimage},
- volume={223},
- pages={117329},
- year={2020},
- publisher={Elsevier}
-}
-Alternatively, an interactive boilerplate generator is available in the documentation website.
-