ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies

Mutsaerts, Henk‐Jan; Petr, Jan; Groot, Paul F. C.; Vandemaele, Pieter; Ingala, Silvia; Robertson, Andrew D.; Václavů, Lena; Groote, Inge Rasmus; Kuijf, Hugo J.; Zelaya, Fernando; O’Daly, Owen; Hilal, Saima; Wink, Alle Meije; Kant, Ilse; Caan, Matthan W.A.; Morgan, Catherine A.; Bresser, Jeroen de; Lysvik, Elisabeth Kirkeby; Schrantee, Anouk; Bjørnebekk, Astrid; Clement, Patricia; Shirzadi, Zahra; Kuijer, Joost P.A.; Wottschel, Viktor; Anazodo, Udunna; Pajkrt, Dasja; Richard, Edo; Bokkers, Reinoud P H; Reneman, Liesbeth; Masellis, Mario; Günther, Matthias; MacIntosh, Bradley J.; Achten, Eric; Chappell, Michael A.; Osch, Matthias J.P. van; Golay, Xavier; Thomas, David L.; Vita, Enrico De; Bjørnerud, Atle; Nederveen, Aart J.; Hendrikse, Jeroen; Asllani, Iris; Barkhof, Frederik

doi:10.1016/j.neuroimage.2020.117031

Cited by 87 publications

(124 citation statements)

References 127 publications

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“…Preprocessing of ASL data was performed with the ExploreASL pipeline 5 and consisted of motion correction, exclusion of motion outliers using the ENABLE algorithm 17 , CBF quantification according to the consensus paper 4 , and partial volume correction by linear regression 18 . We calculated a voxelwise between-hemisphere asymmetry index (AI) ) of the CBF maps in voxel x 19 : AIx = 100*( CBFx -CBFy) / (CBFx + CBFy)…”

Section: Data Preprocessingmentioning

confidence: 99%

“…ASL is generally accessible as a product sequence on most MRI machines, is completely non-invasive, and has clinically feasible scanning times. Recent progress in the standardization of ASL acquisition 4 , data sharing, and processing 5 , made this a common tool for clinical research with increasing adoption into clinical practice 6 . ASL was demonstrated to be helpful in several types of epilepsy, including e.g.…”

Section: Introductionmentioning

confidence: 99%

“…temporal lobe epilepsy 7,8 and frontal lobe epilepsy 8,9 . One major remaining hurdle to the application of ASL as detection of EZ, is the definition of EZ on ASL perfusion images in a robust way; especially considering the physiological variability between patients 10 and inter-scanner quantification challenges 5 . In this study, we focused on EZ detection in MRI-negative epilepsy based on ASL data.…”

Section: Introductionmentioning

confidence: 99%

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Arterial spin labeling: Adaptive thresholding for epileptogenic zone detection in MRI-negative epilepsy

Gajdoš

Říha

Kojan

et al. 2021

Preprint

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Drug-resistant epilepsy is a diagnostic and therapeutic challenge, mainly in patients with negative MRI findings. State-of-the-art imaging methods complement standard epilepsy protocols with new information and help to epileptologists to increase reliability of their decisions. In this study, we investigate if arterial spin labeling (ASL) perfusion MRI can help localizing the epileptogenic zone (EZ). To that end, we developed an image processing method to detect the EZ as an area with hypoperfusion relative to the contralateral unaffected side, using subject-specific thresholding of the asymmetry index in ASL images. We demonstrated three thresholding criteria (minimal product criterion, minimal distance criterion, and elbow criterion) on 29 patients with MRI-negative epilepsy (age 32.98 ± 10.4 years). The minimal product criterion showed optimal results in terms of positive predictive value (mean 0.12 and 0.22) and true positive rate (mean 0.71 and 1.82). Additionally, we found high accuracy in determining the EZ side (mean 0.86 and 0.73 out of 1.00). In conclusion, the ASL can be easily incorporated to the standard presurgical MR protocol and it provides an additional benefit in EZ localization.

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Section: Data Preprocessingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Arterial spin labeling: Adaptive thresholding for epileptogenic zone detection in MRI-negative epilepsy

Gajdoš

Říha

Kojan

et al. 2021

Preprint

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“…These endeavours comprise not only formulating recommendations for conventional MRI [50], but also for advanced MRI techniques in certain targeted patient populations. More specifically, this includes consensus recommendations for DSC in high-grade gliomas [51], brain perfusion imaging acquisition and processing recommendations for ASL [52,53], or functional (f)MRI recommendations for pre-treatment planning and follow-up [54]. Despite such efforts, approaches for the harmonisation of data acquisition, recommendations for the optimal combination of MRI-biomarkers, and standardised open-source data analysis software for post-processing are currently not widely accepted, implemented or available.…”

Section: Lack Of Harmonization Hampers Widespread Use In Research Andmentioning

confidence: 99%

“…Current knowledge on the most pertinent, existing, advanced MRI biomarkers and the methods to combine those with data from psychological assessments, genetics, and histology, as well as the technology readiness level of current data analysis methods, will be assessed by reviewing the state-of-the-art literature. As an example, the ASLanalysis toolbox ExploreASL has recently been launched, allowing the pooling of multi-centre ASL datasets, increasing comparability and narrowing the gap between clinicians, researchers and developers [53]. Special attention will be given to identify existing gaps in the current analysis and use of glioma biomarkers, which is in line with the goals of QIN [46] and OSIPI [49].…”

Section: Ca18206: Glioma Mr Imaging 20mentioning

confidence: 99%

GliMR: Cross-Border Collaborations to Promote Advanced MRI Biomarkers for Glioma

et al. 2020

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Purpose There is an annual incidence of 50,000 glioma cases in Europe. The optimal treatment strategy is highly personalised, depending on tumour type, grade, spatial localization, and the degree of tissue infiltration. In research settings, advanced magnetic resonance imaging (MRI) has shown great promise as a tool to inform personalised treatment decisions. However, the use of advanced MRI in clinical practice remains scarce due to the downstream effects of siloed glioma imaging research with limited representation of MRI specialists in established consortia; and the associated lack of available tools and expertise in clinical settings. These shortcomings delay the translation of scientific breakthroughs into novel treatment strategy. As a response we have developed the network “Glioma MR Imaging 2.0” (GliMR) which we present in this article. Methods GliMR aims to build a pan-European and multidisciplinary network of experts and accelerate the use of advanced MRI in glioma beyond the current “state-of-the-art” in glioma imaging. The Action Glioma MR Imaging 2.0 (GliMR) was granted funding by the European Cooperation in Science and Technology (COST) in June 2019. Results GliMR’s first grant period ran from September 2019 to April 2020, during which several meetings were held and projects were initiated, such as reviewing the current knowledge on advanced MRI; developing a General Data Protection Regulation (GDPR) compliant consent form; and setting up the website. Conclusion The Action overcomes the pre-existing limitations of glioma research and is funded until September 2023. New members will be accepted during its entire duration.

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Long-Term Brain Structure and Cognition Following Bariatric Surgery

Custers,

Vreeken,

Kleemann

et al. 2024

JAMA Netw Open

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ImportanceWeight loss induced by bariatric surgery (BS) is associated with improved cognition and changed brain structure; however, previous studies on the association have used small cohorts and short follow-up periods, making it difficult to determine long-term neurological outcomes associated with BS.ObjectiveTo investigate long-term associations of weight loss after BS with cognition and brain structure and perfusion.Design, Setting, and ParticipantsThis cohort study included participants from the Bariatric Surgery Rijnstate and Radboudumc Neuroimaging and Cognition in Obesity study. Data from participants with severe obesity (body mass index [BMI; calculated as weight in kilograms divided by height in meters squared] &gt;40, or BMI &gt;35 with comorbidities) eligible for Roux-en-Y gastric bypass and aged 35 to 55 years were enrolled from a hospital specialized in BS (Rijnstate Hospital, Arnhem, the Netherlands). Participants were recruited between September 2018 and December 2020 with follow-up till March 2023. Data were collected before BS and at 6 and 24 months after BS. Data were analyzed from March to November 2023.ExposureRoux-en-Y gastric bypass.Main Outcomes and MeasuresPrimary outcomes included body weight, BMI, waist circumference, blood pressure, medication use, cognitive performance (20% change index of compound z-score), brain volumes, cortical thickness, cerebral blood flow (CBF), and spatial coefficient of variation (sCOV). Secondary outcomes include cytokines, adipokines, depressive symptoms (assessed using the Beck Depression Inventory), and physical activity (assessed using the Baecke Questionnaire).ResultsA total of 133 participants (mean [SD] age, 46.8 [5.7] years; 112 [84.2%] female) were included. Global cognition was at least 20% higher in 52 participants (42.9%) at 24 months after BS. Compared with baseline, at 24 months, inflammatory markers were lower (mean [SD] high-sensitivity C-reactive protein: 4.77 [5.80] μg/mL vs 0.80 [1.09] μg/mL; P &lt; .001), fewer patients used antihypertensives (48 patients [36.1%] vs 22 patients [16.7%]), and patients had lower depressive symptoms (median [IQR] BDI score: 9.0 [5.0-13.0] vs 3.0 [1.0-6.0]; P &lt; .001) and greater physical activity (mean [SD] Baecke score: 7.64 [1.29] vs 8.19 [1.35]; P &lt; .001). After BS, brain structure and perfusion were lower in most brain regions, while hippocampal and white matter volume remained stable. CBF and sCOV did not change in nucleus accumbens and parietal cortex. The temporal cortex showed a greater thickness (mean [SD] thickness: 2.724 [0.101] mm vs 2.761 [0.007] mm; P = .007) and lower sCOV (median [IQR] sCOV: 4.41% [3.83%-5.18%] vs 3.97% [3.71%-4.59%]; P = .02) after BS.Conclusions and RelevanceThese findings suggest that BS was associated with health benefits 2 years after surgery. BS was associated with improved cognition and general health and changed blood vessel efficiency and cortical thickness of the temporal cortex. These results may improve treatment options for patients with obesity and dementia.

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ExploreASL: An image processing pipeline for multi-center ASL perfusion MRI studies

Cited by 87 publications

References 127 publications

Arterial spin labeling: Adaptive thresholding for epileptogenic zone detection in MRI-negative epilepsy

Arterial spin labeling: Adaptive thresholding for epileptogenic zone detection in MRI-negative epilepsy

GliMR: Cross-Border Collaborations to Promote Advanced MRI Biomarkers for Glioma

Long-Term Brain Structure and Cognition Following Bariatric Surgery

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