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LAYER FMRI BLOG
Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020:SETTING UP LAYNII
LAYER-FMRI PAPERS
Layer fMRI papers. This page depicts a collection of all layer-fMRI papers. This list only includes papers that focus on: cortical layer-fMRI in humans. Preprints are included. Suggestions are welcome layerfMRI@gmail.com. For non-cortical, non-fMRI, non-human, or non-layer high resolution MRI, please see reviews in special issues 1,2, 3 (and
THIRD VIRTUAL LAYER-FMRI ‘DINNER’: COGNITIVE MODELS AND Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020: ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
REGISTRATION OF HIGH-RESOLUTION DATA In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences. I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms. UNWANTED SPATIAL BLURRING DURING RESAMPLING Unwanted spatial blurring during resampling. renzohuber code March 23, 2018. May 20, 2018. 6 Minutes. In layer-fMRI, we spend so much time and effort to achieve high spatial resolutions and small voxel sizes during the acquisition. However, during the evaluation pipeline much of this spatial resolution can be lost during multiple resamplingsteps.
SS-SI VASO PITFALLS IN VISUAL CORTEX SS-SI VASO pitfalls in visual cortex. Activation maps for BOLD and VASO. At about 0.8 mm resolution, one starts to see that VASO is less sensitive to large draining veins. With respect to high-resolution VASO application, visual cortex is very unique. I found it to be achallenging area.
RENZOS POWER-POINT SLIDE REPOSITORY Renzos Power-Point Slide Repository. This post contains a collection of recently presented powerpoint slides. Huber L, Merriam E, Kim I, Chai Yuhui, Kashyap S, Polimeni J, Roth Z, Shim WM, Kim SG, Ivanov D, PoserB, Bandettini P, (2019) Measuring layer-dependent CBV fMRI in the visual system, 0399, ISMRM, Slides, Video.LAYER FMRI BLOG
Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020:SETTING UP LAYNII
LAYER-FMRI PAPERS
Layer fMRI papers. This page depicts a collection of all layer-fMRI papers. This list only includes papers that focus on: cortical layer-fMRI in humans. Preprints are included. Suggestions are welcome layerfMRI@gmail.com. For non-cortical, non-fMRI, non-human, or non-layer high resolution MRI, please see reviews in special issues 1,2, 3 (and
THIRD VIRTUAL LAYER-FMRI ‘DINNER’: COGNITIVE MODELS AND Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020: ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
REGISTRATION OF HIGH-RESOLUTION DATA In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences. I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms. UNWANTED SPATIAL BLURRING DURING RESAMPLING Unwanted spatial blurring during resampling. renzohuber code March 23, 2018. May 20, 2018. 6 Minutes. In layer-fMRI, we spend so much time and effort to achieve high spatial resolutions and small voxel sizes during the acquisition. However, during the evaluation pipeline much of this spatial resolution can be lost during multiple resamplingsteps.
SS-SI VASO PITFALLS IN VISUAL CORTEX SS-SI VASO pitfalls in visual cortex. Activation maps for BOLD and VASO. At about 0.8 mm resolution, one starts to see that VASO is less sensitive to large draining veins. With respect to high-resolution VASO application, visual cortex is very unique. I found it to be achallenging area.
RENZOS POWER-POINT SLIDE REPOSITORY Renzos Power-Point Slide Repository. This post contains a collection of recently presented powerpoint slides. Huber L, Merriam E, Kim I, Chai Yuhui, Kashyap S, Polimeni J, Roth Z, Shim WM, Kim SG, Ivanov D, PoserB, Bandettini P, (2019) Measuring layer-dependent CBV fMRI in the visual system, 0399, ISMRM, Slides, Video. ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin TUTORIALS – LAYER FMRI BLOG This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain LAYNII – LAYER FMRI BLOG With respect to applying equi-volume principle in layer-fMRI, the equi-volume layering has gone through quite a story. A plot with many parallels to Anakin Skywalker. In this blog, the equi-volume layering approach is evaluated. Furthermore, it is demonstrated how to use it CODE – LAYER FMRI BLOG This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain “anatomical” datasets, or automatic tissue type segmentation. BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
LAYER-FMRI VASO WORLDWIDE Layer-fMRI VASO worldwide. This blog post gives an overview of the scientific network of researchers that are using the VASO (vascular space occupancy) for applications in layer-fMRI. I tried to give an overview of all layer-fMRI VASO papers published so far and provide a map of all layer-fMRI VASO labs around the globe. QUALITY ASSURANCE MEASURES FOR LAYER-FMRI TIME SERIES: HOW Doing layer-fMRI sometimes feels like doing nothing more than noise management. One must have a full grown masochistic personality trait to enjoy working with such messy data. Namely, layer-fMRI time series data suffer from each and every one of the artifacts in conventional fMRI; they are just much worse and there are also a few QUICK ANALYSIS PIPELINE OF GETTING LAYER FMRI PROFILES This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain "anatomical" datasets, or automatic tissue type segmentation. Hence this is a very quick way for a first FAQ OF THE DZNE VASO SEQUENCE FOR VE The usage of this VB sequence is explained on a different blog post here. While the DZNE sequence is mainly supported for VE, some experimental versions of it can be compiled for VB 17 too. Those VASO versions are not fully vetted (yet) and used for exploratory purposesonly. 10.)
RENZOHUBER – LAYER FMRI BLOG On May 7th 2020, there was a virtual layerfMRI event to discuss current issues in the field. This meeting was held as a replacement of an originally planned layer-fMRI dinner at ISMRM and happened in succession of an earlier in-person layerfMRI workshop in November 2019 (meeting minutes here).Below you find the important links of the the virtual event, videos of the talks and discussions, andLAYER FMRI BLOG
Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020:SETTING UP LAYNII
LAYER-FMRI PAPERS
Layer fMRI papers. This page depicts a collection of all layer-fMRI papers. This list only includes papers that focus on: cortical layer-fMRI in humans. Preprints are included. Suggestions are welcome layerfMRI@gmail.com. For non-cortical, non-fMRI, non-human, or non-layer high resolution MRI, please see reviews in special issues 1,2, 3 (and
THIRD VIRTUAL LAYER-FMRI ‘DINNER’: COGNITIVE MODELS AND Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020: ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
REGISTRATION OF HIGH-RESOLUTION DATA In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences. I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms. UNWANTED SPATIAL BLURRING DURING RESAMPLING Unwanted spatial blurring during resampling. renzohuber code March 23, 2018. May 20, 2018. 6 Minutes. In layer-fMRI, we spend so much time and effort to achieve high spatial resolutions and small voxel sizes during the acquisition. However, during the evaluation pipeline much of this spatial resolution can be lost during multiple resamplingsteps.
SS-SI VASO PITFALLS IN VISUAL CORTEX SS-SI VASO pitfalls in visual cortex. Activation maps for BOLD and VASO. At about 0.8 mm resolution, one starts to see that VASO is less sensitive to large draining veins. With respect to high-resolution VASO application, visual cortex is very unique. I found it to be achallenging area.
RENZOS POWER-POINT SLIDE REPOSITORY Renzos Power-Point Slide Repository. This post contains a collection of recently presented powerpoint slides. Huber L, Merriam E, Kim I, Chai Yuhui, Kashyap S, Polimeni J, Roth Z, Shim WM, Kim SG, Ivanov D, PoserB, Bandettini P, (2019) Measuring layer-dependent CBV fMRI in the visual system, 0399, ISMRM, Slides, Video.LAYER FMRI BLOG
Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020:SETTING UP LAYNII
LAYER-FMRI PAPERS
Layer fMRI papers. This page depicts a collection of all layer-fMRI papers. This list only includes papers that focus on: cortical layer-fMRI in humans. Preprints are included. Suggestions are welcome layerfMRI@gmail.com. For non-cortical, non-fMRI, non-human, or non-layer high resolution MRI, please see reviews in special issues 1,2, 3 (and
THIRD VIRTUAL LAYER-FMRI ‘DINNER’: COGNITIVE MODELS AND Third Virtual Layer-fMRI ‘Dinner’: Cognitive Models and Cortical Layers. On April 20th 2021, the third virtual layer-fMRI took place. 120 (unique) attendees joined and discussed the connection between layer-fMRI and cognitive models. This meeting is held as a succession of the first two virtual dinner in May 2020, and Sept 2020: ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
REGISTRATION OF HIGH-RESOLUTION DATA In this blog post Sri Kashyap and I describe how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences. I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms. UNWANTED SPATIAL BLURRING DURING RESAMPLING Unwanted spatial blurring during resampling. renzohuber code March 23, 2018. May 20, 2018. 6 Minutes. In layer-fMRI, we spend so much time and effort to achieve high spatial resolutions and small voxel sizes during the acquisition. However, during the evaluation pipeline much of this spatial resolution can be lost during multiple resamplingsteps.
SS-SI VASO PITFALLS IN VISUAL CORTEX SS-SI VASO pitfalls in visual cortex. Activation maps for BOLD and VASO. At about 0.8 mm resolution, one starts to see that VASO is less sensitive to large draining veins. With respect to high-resolution VASO application, visual cortex is very unique. I found it to be achallenging area.
RENZOS POWER-POINT SLIDE REPOSITORY Renzos Power-Point Slide Repository. This post contains a collection of recently presented powerpoint slides. Huber L, Merriam E, Kim I, Chai Yuhui, Kashyap S, Polimeni J, Roth Z, Shim WM, Kim SG, Ivanov D, PoserB, Bandettini P, (2019) Measuring layer-dependent CBV fMRI in the visual system, 0399, ISMRM, Slides, Video. ABOUT – LAYER FMRI BLOG Other references: Twitter @layerfMRI High-field scanner google-map Github layerfMRI Youtube layerfMRI Lab home page at MR-Methods List of layer-fMRI papers in humans Layer-fMRI Tshirts to buy onlin TUTORIALS – LAYER FMRI BLOG This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain LAYNII – LAYER FMRI BLOG With respect to applying equi-volume principle in layer-fMRI, the equi-volume layering has gone through quite a story. A plot with many parallels to Anakin Skywalker. In this blog, the equi-volume layering approach is evaluated. Furthermore, it is demonstrated how to use it CODE – LAYER FMRI BLOG This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain “anatomical” datasets, or automatic tissue type segmentation. BASELINE CBV AND IT’S ROLE FOR THE INTERPRETATION OF LAYER The single most cited study of baseline CBV values is the PET study from Leenders et al. in 1990. This study finds values of 4.3 – 8.6 ml per 100 ml of cortical gray matter tissue.; CBV values estimated with PET in: Leenders KL, Perani D, Lammertsma A, et al. Cerebral blood flow, blood volume and oxygen utilization.Normal values andeffect of age.
LAYER-FMRI VASO WORLDWIDE Layer-fMRI VASO worldwide. This blog post gives an overview of the scientific network of researchers that are using the VASO (vascular space occupancy) for applications in layer-fMRI. I tried to give an overview of all layer-fMRI VASO papers published so far and provide a map of all layer-fMRI VASO labs around the globe. QUALITY ASSURANCE MEASURES FOR LAYER-FMRI TIME SERIES: HOW Doing layer-fMRI sometimes feels like doing nothing more than noise management. One must have a full grown masochistic personality trait to enjoy working with such messy data. Namely, layer-fMRI time series data suffer from each and every one of the artifacts in conventional fMRI; they are just much worse and there are also a few QUICK ANALYSIS PIPELINE OF GETTING LAYER FMRI PROFILES This is a step-by-step description on how to obtain layer profiles from any high-resolution fMRI dataset. It is based on manual delineated ROIs and does not require the tricky analysis steps including distortion correction, registration to whole brain "anatomical" datasets, or automatic tissue type segmentation. Hence this is a very quick way for a first FAQ OF THE DZNE VASO SEQUENCE FOR VE The usage of this VB sequence is explained on a different blog post here. While the DZNE sequence is mainly supported for VE, some experimental versions of it can be compiled for VB 17 too. Those VASO versions are not fully vetted (yet) and used for exploratory purposesonly. 10.)
RENZOHUBER – LAYER FMRI BLOG On May 7th 2020, there was a virtual layerfMRI event to discuss current issues in the field. This meeting was held as a replacement of an originally planned layer-fMRI dinner at ISMRM and happened in succession of an earlier in-person layerfMRI workshop in November 2019 (meeting minutes here).Below you find the important links of the the virtual event, videos of the talks and discussions, andSkip to content
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MP2RAGE: CHALLENGES AND ARTIFACTS OF ITS USE FOR LAYER-FMRI The MP2RAGE sequence is very popular for 7T anatomical imaging and is very commonly used to acquire 0.7-1 mm resolution whole brain anatomical reference data. Aside of this common application, it can also be very helpful for layer-fMRI studies to obtain even higher resolution T1 maps in the range of 0.5mm iso. However, when optimizing MP2RAGE sequence parameters for layer-fMRI studies, there are a few things that might be helpful to keep in mind. In this post, I would like to discuss the challenges of using the popular MP2RAGE sequence in layer-fMRI studies. Specifically I will discuss challenges/features regarding:* Background noise.
* Foldover artifact at very high resolutions. * Usage of double-partial Fourier imaging. * Inflow into arterial vessels. Continue reading “MP2RAGE: challenges and artifacts of its use for layer-fMRI” →SHARE THIS:
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June 22, 2019July
5, 2019 7 Minutes
LAYER-FMRI ABSTRACTS AT OHBM/ISMRM 2019 The following is a personal selection of my must-see layer-fMRI abstracts presented at OHBM/ISMRM 2019. If I missed something, please let me know (layerfMRI@gmail.com). Continue reading “layer-fMRI abstracts at OHBM/ISMRM 2019” →SHARE THIS:
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April 17, 2019June 4, 20194 Minutes
EXAMPLE ANALYSIS PIPELINE OF LAYER-VASO In this blog post I want to go through the analysis pipeline of layer-dependent VASO. I will go through the all the analysis steps that need to be done to go from raw data from the scanner to final layer profiles. The entire thing will take about 30 min (10 min analysis and 20 min explaining and browsing through data). During the entire analysis pipeline I am using the following software packages: SPM , AFNI, and LAYNII
, and gnuplot (if you want fancier plotting tools) Continue reading “Example analysis pipeline of layer-VASO” →SHARE THIS:
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March
22, 2019March 25, 20193 Minutes
HOW MANY LAYERS SHOULD I EXTRACT? In this blog post, I want to share my thoughts on the number of layers that should be extracted from any given dataset. I will try to give an overview of how many layers are usually extracted in the field, I’ll describe my personal choices of layer numbers, and I will try to discuss the challenges of layer signal extraction along the way. Continue reading “How many layers should I extract?” →SHARE THIS:
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February 22, 2019March 5, 20199 Minutes
‘LAYER FMRI’, ‘SUB-MILLIMETER FMRI’, ‘MESOSCOPIC FMRI’, OR ‘CORTICAL DEPTH DEPENDENT FMRI’…. WHICH TERM SHOULD I USE? What’s the best name of our field and what’s the best attributing term for our data? There are many competing options: “Layer fMRI”, “mesoscopic fMRI”, “sub-millimeter fMRI”, “ultra-high resolution fMRI”, “laminar fMRI”, “cortical depth-dependent fMRI”. They differ with respect to how flashy they are, how scientifically appropriate they are, and how popular they are. In this blog post, I want to review which ones are the most popular ones in the field and also share some thoughts on my favouritecandidates.
Edits on March 3rd 2019 with contributions and clarifications taken from Kamil Uludağ, Sri Kashyap and Faruk Gulban. Continue reading “‘layer fMRI’, ‘sub-millimeter fMRI’, ‘mesoscopic fMRI’, or ‘cortical depth dependent fMRI’…. Which term should I use?” →SHARE THIS:
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February 21,
2019June 27, 2019 12Minutes
REGISTRATION OF HIGH-RESOLUTION DATA In this blog post Sri Kashyapand I describe
how to deal with the registration of high-resolution datasets across days, across different resolutions, and across different sequences. I am particularly fond of the following two tools: Firstly, ITK-SNAP for visually-guided manual alignment and secondly, using ANTs programs: antsRegistration and antsApplyTransforms. Continue reading “Registration of high-resolution data” →SHARE THIS:
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February 11, 2019April 24, 20193
Minutes
INTENSITY PROJECTIONS IN LAYNII Maximum intensity projection and minimum intensity projection can be insightful for mapping of vessels in 3D-slabs. In this post, I describe the application of intensity projections with LAYNII. Continue reading “Intensity projections in LAYNII” →SHARE THIS:
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February 5, 2019February 5, 20191
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