Quality control in functional MRI studies with MRIQC and fMRIPrep

Removing facial features from structural MRI images biases visual quality assessment

A critical step before data-sharing of human neuroimaging is removing facial features to protect individuals' privacy. However, not only does this process redact identifiable information about individuals, but it also removes non-identifiable information. This introduces undesired variability into downstream analysis and interpretation. This registered report investigated the degree to which the so-called defacing altered the quality assessment of T1-weighted images of the human brain from the openly available "IXI dataset". The effect of defacing on manual quality assessment was investigated on a single-site subset of the dataset (N = 185). By comparing two linear mixed-effects models, we determined that four trained human raters' perception of quality was significantly influenced by defacing by modeling their ratings on the same set of images in two conditions: "nondefaced" (i.e., preserving facial features) and "defaced". In addition, we investigated these biases on automated quality assessments by applying repeated-measures, multivariate ANOVA (rm-MANOVA) on the image quality metrics extracted with MRIQC on the full IXI dataset (N = 581; three acquisition sites). This study found that defacing altered the quality assessments by humans and showed that MRIQC's quality metrics were mostly insensitive to defacing.

Defacing biases visual quality assessments of structural MRI

A critical step before data-sharing of human neuroimaging is removing facial features to protect individuals' privacy. However, not only does this process redact identifiable information about individuals, but it also removes non-identifiable information. This introduces undesired variability into downstream analysis and interpretation. This registered report investigated the degree to which the so-called defacing altered the quality assessment of T1-weighted images of the human brain from the openly available "IXI dataset". The effect of defacing on manual quality assessment was investigated on a single-site subset of the dataset (N=185). By comparing two linear mixed-effects models, we determined that four trained human raters' perception of quality was significantly influenced by defacing by modeling their ratings on the same set of images in two conditions: "nondefaced" (i.e., preserving facial features) and "defaced". In addition, we investigated these biases on automated quality assessments by applying repeated-measures, multivariate ANOVA (rm-MANOVA) on the image quality metrics extracted with MRIQC on the full IXI dataset (N=581; three acquisition sites). This study found that defacing altered the quality assessments by humans and showed that MRIQC's quality metrics were mostly insensitive to defacing.

Quality assessment and control of unprocessed anatomical, functional, and diffusion MRI of the human brain using MRIQC

Quality control of MRI data prior to preprocessing is fundamental, as substandard data are known to increase variability spuriously. Currently, no automated or manual method reliably identifies subpar images, given pre-specified exclusion criteria. In this work, we propose a protocol describing how to carry out the visual assessment of T1-weighted, T2-weighted, functional, and diffusion MRI scans of the human brain with the visual reports generated by MRIQC. The protocol describes how to execute the software on all the images of the input dataset using typical research settings (i.e., a high-performance computing cluster). We then describe how to screen the visual reports generated with MRIQC to identify artifacts and potential quality issues and annotate the latter with the "rating widget" ─ a utility that enables rapid annotation and minimizes bookkeeping errors. Integrating proper quality control checks on the unprocessed data is fundamental to producing reliable statistical results and crucial to identifying faults in the scanning settings, preempting the acquisition of large datasets with persistent artifacts that should have been addressed as they emerged.

Targeted memory reactivation to augment treatment in post-traumatic stress disorder

Post-traumatic stress disorder (PTSD) is a psychiatric disorder with traumatic memories at its core. Post-treatment sleep may offer a unique time window to increase therapeutic efficacy through consolidation of therapeutically modified traumatic memories. Targeted memory reactivation (TMR) enhances memory consolidation by presenting reminder cues (e.g., sounds associated with a memory) during sleep. Here, we applied TMR in PTSD patients to strengthen therapeutic memories during sleep after one treatment session with eye movement desensitization and reprocessing (EMDR). PTSD patients received either slow oscillation (SO) phase-targeted TMR, using modeling-based closed-loop neurostimulation (M-CLNS) with EMDR clicks as a reactivation cue (n = 17), or sham stimulation (n = 16). Effects of TMR on sleep were assessed through high-density polysomnography. Effects on treatment outcome were assessed through subjective, autonomic, and fMRI responses to script-driven imagery (SDI) of the targeted traumatic memory and overall PTSD symptom level. Compared to sham stimulation, TMR led to stimulus-locked increases in SO and spindle dynamics, which correlated positively with PTSD symptom reduction in the TMR group. Given the role of SOs and spindles in memory consolidation, these findings suggest that TMR may have strengthened the consolidation of the EMDR-treatment memory. Clinically, TMR vs. sham stimulation resulted in a larger reduction of avoidance level during SDI. TMR did not disturb sleep or trigger nightmares. Together, these data provide first proof of principle that TMR may be a safe and viable future treatment augmentation strategy for PTSD. The required follow-up studies may implement multi-night TMR or TMR during REM sleep to further establish the clinical effect of TMR for traumatic memories.

A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth, and interactive QC with afni_proc.py and more

Quality control (QC) assessment is a vital part of FMRI processing and analysis, and a typically underdiscussed aspect of reproducibility. This includes checking datasets at their very earliest stages (acquisition and conversion) through their processing steps (e.g., alignment and motion correction) to regression modeling (correct stimuli, no collinearity, valid fits, enough degrees of freedom, etc.) for each subject. There are a wide variety of features to verify throughout any single-subject processing pipeline, both quantitatively and qualitatively. We present several FMRI preprocessing QC features available in the AFNI toolbox, many of which are automatically generated by the pipeline-creation tool, afni_proc.py. These items include a modular HTML document that covers full single-subject processing from the raw data through statistical modeling, several review scripts in the results directory of processed data, and command line tools for identifying subjects with one or more quantitative properties across a group (such as triaging warnings, making exclusion criteria, or creating informational tables). The HTML itself contains several buttons that efficiently facilitate interactive investigations into the data, when deeper checks are needed beyond the systematic images. The pages are linkable, so that users can evaluate individual items across a group, for increased sensitivity to differences (e.g., in alignment or regression modeling images). Finally, the QC document contains rating buttons for each "QC block," as well as comment fields for each, to facilitate both saving and sharing the evaluations. This increases the specificity of QC, as well as its shareability, as these files can be shared with others and potentially uploaded into repositories, promoting transparency and open science. We describe the features and applications of these QC tools for FMRI.

Solving the Pervasive Problem of Protocol Non-Compliance in MRI using an Open-Source tool mrQA

Pooling data across diverse sources acquired by multisite consortia requires compliance with a predefined reference protocol i.e., ensuring different sites and scanners for a given project have used identical or compatible MR physics parameter values. Traditionally, this has been an arduous and manual process due to difficulties in working with the complicated DICOM standard and lack of resources allocated towards protocol compliance. Moreover, issues of protocol compliance is often overlooked for lack of realization that parameter values are routinely improvised/modified locally at various sites. The inconsistencies in acquisition protocols can reduce SNR, statistical power, and in the worst case, may invalidate the results altogether. An open-source tool, mrQA was developed to automatically assess protocol compliance on standard dataset formats such as DICOM and BIDS, and to study the patterns of non-compliance in over 20 open neuroimaging datasets, including the large ABCD study. The results demonstrate that the lack of compliance is rather pervasive. The frequent sources of non-compliance include but are not limited to deviations in Repetition Time, Echo Time, Flip Angle, and Phase Encoding Direction. It was also observed that GE and Philips scanners exhibited higher rates of non-compliance relative to the Siemens scanners in the ABCD dataset. Continuous monitoring for protocol compliance is strongly recommended before any pre/post-processing, ideally right after the acquisition, to avoid the silent propagation of severe/subtle issues. Although, this study focuses on neuroimaging datasets, the proposed tool mrQA can work with any DICOM-based datasets.

A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth and interactive QC with afni_proc.py and more

Quality control (QC) assessment is a vital part of FMRI processing and analysis, and a typically under-discussed aspect of reproducibility. This includes checking datasets at their very earliest stages (acquisition and conversion) through their processing steps (e.g., alignment and motion correction) to regression modeling (correct stimuli, no collinearity, valid fits, enough degrees of freedom, etc.) for each subject. There are a wide variety of features to verify throughout any single subject processing pipeline, both quantitatively and qualitatively. We present several FMRI preprocessing QC features available in the AFNI toolbox, many of which are automatically generated by the pipeline-creation tool, afni_proc.py. These items include: a modular HTML document that covers full single subject processing from the raw data through statistical modeling; several review scripts in the results directory of processed data; and command line tools for identifying subjects with one or more quantitative properties across a group (such as triaging warnings, making exclusion criteria or creating informational tables). The HTML itself contains several buttons that efficiently facilitate interactive investigations into the data, when deeper checks are needed beyond the systematic images. The pages are linkable, so that users can evaluate individual items across a group, for increased sensitivity to differences (e.g., in alignment or regression modeling images). Finally, the QC document contains rating buttons for each "QC block", as well as comment fields for each, to facilitate both saving and sharing the evaluations. This increases the specificity of QC, as well as its shareability, as these files can be shared with others and potentially uploaded into repositories, promoting transparency and open science. We describe the features and applications of these QC tools for FMRI.

Swin Transformer and the Unet Architecture to Correct Motion Artifacts in Magnetic Resonance Image Reconstruction

We present a deep learning-based method that corrects motion artifacts and thus accelerates data acquisition and reconstruction of magnetic resonance images. The novel model, the Motion Artifact Correction by Swin Network (MACS-Net), uses a Swin transformer layer as the fundamental block and the Unet architecture as the neural network backbone. We employ a hierarchical transformer with shifted windows to extract multiscale contextual features during encoding. A new dual upsampling technique is employed to enhance the spatial resolutions of feature maps in the Swin transformer-based decoder layer. A raw magnetic resonance imaging dataset is used for network training and testing; the data contain various motion artifacts with ground truth images of the same subjects. The results were compared to six state-of-the-art MRI image motion correction methods using two types of motions. When motions were brief (within 5 s), the method reduced the average normalized root mean square error (NRMSE) from 45.25% to 17.51%, increased the mean structural similarity index measure (SSIM) from 79.43% to 91.72%, and increased the peak signal-to-noise ratio (PSNR) from 18.24 to 26.57 dB. Similarly, when motions were extended from 5 to 10 s, our approach decreased the average NRMSE from 60.30% to 21.04%, improved the mean SSIM from 33.86% to 90.33%, and increased the PSNR from 15.64 to 24.99 dB. The anatomical structures of the corrected images and the motion-free brain data were similar.

Mindfulness-based real-time fMRI neurofeedback: a randomized controlled trial to optimize dosing for depressed adolescents

BACKGROUND

Adolescence is characterized by a heightened vulnerability for Major Depressive Disorder (MDD) onset, and currently, treatments are only effective for roughly half of adolescents with MDD. Accordingly, novel interventions are urgently needed. This study aims to establish mindfulness-based real-time fMRI neurofeedback (mbNF) as a non-invasive approach to downregulate the default mode network (DMN) in order to decrease ruminatory processes and depressive symptoms.

METHODS

Adolescents (N = 90) with a current diagnosis of MDD ages 13-18-years-old will be randomized in a parallel group, two-arm, superiority trial to receive either 15 or 30 min of mbNF with a 1:1 allocation ratio. Real-time neurofeedback based on activation of the frontoparietal network (FPN) relative to the DMN will be displayed to participants via the movement of a ball on a computer screen while participants practice mindfulness in the scanner. We hypothesize that within-DMN (medial prefrontal cortex [mPFC] with posterior cingulate cortex [PCC]) functional connectivity will be reduced following mbNF (Aim 1: Target Engagement). Additionally, we hypothesize that participants in the 30-min mbNF condition will show greater reductions in within-DMN functional connectivity (Aim 2: Dosing Impact on Target Engagement). Aim 1 will analyze data from all participants as a single-group, and Aim 2 will leverage the randomized assignment to analyze data as a parallel-group trial. Secondary analyses will probe changes in depressive symptoms and rumination.

DISCUSSION

Results of this study will determine whether mbNF reduces functional connectivity within the DMN among adolescents with MDD, and critically, will identify the optimal dosing with respect to DMN modulation as well as reduction in depressive symptoms and rumination.

TRIAL REGISTRATION

This study has been registered with clinicaltrials.gov, most recently updated on July 6, 2023 (trial identifier: NCT05617495).