MethControl

AFNI is an open source software package for the analysis and display of functional MRI data. It originated in 1994 to meet the specific needs of resea…

For those of you without access to a Unix-based platform, or whether you are just having a difficult time correctly installing your Python l...

Scripts used for fMRI data analysis in AFNI. Contribute to andrewjahn/AFNI_Scripts development by creating an account on GitHub.

Hi, I am currently writing some packages for AFNI/FSL/SPM for my favourite distro (Gentoo). I plan to use these toolkits via nipype. On the example of AFNI: I am currently placing everything into /...

CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Abstract: The Functional Imaging Analysis Contest (FIAC) datasets were analyzed with the AFNI software package. Two types of linear regression analyses were carried out: “fixed shape ” hemodynamic response, where a preselected incomplete gamma function is used to model each brief activation episode, and “variable shape ” analysis, where the temporal shape of the response model in each stimulus block class is allowed to vary separately in each voxel. These time series regressions were carried out both in the volume and on the original data projected to individual standardized cortical surface models. Intersubject analyses were carried out voxel-wise on the regression amplitudes obtained from these time series results, using a multi-way within-subject analysis of variance (ANOVA). Group analysis of the block design demonstrated a significant repetition suppression of the BOLD signal within blocks in the superior and middle temporal gyrus. This effect may represent differences in the response to the first stimulus following a period of silence compared to the remaining sentences in the block. Analyzing the event-related data, Brodmann area 31 showed significant sentence effect and consecutive-sentence repetition effect. However, no significant speaker effect was found; these results may be consistent with the instructions to the subjects that they would be tested on the sentence content. Sentence by speaker interaction effects were found in bilateral middle temporal gyrus, left inferior frontal, and left inferior

CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Surface-based brain imaging analysis is increasingly being used for detailed analysis of the topology of brain activation patterns and changes in cerebral gray matter. Here we present SUMA, a new interface for visualizing and performing surfacebased brain imaging analysis that is tightly coupled to AFNI – a volume-based brain imaging analysis suite. The interactive part of SUMA is used for rapid and interactive surface and data visualization, access and manipulations with direct link to the volumetric data rendered in AFNI. The batch-mode part of SUMA allows for surface based operations such as geometry and data smoothing [1, 2], surface to volume domain mapping in both directions and node-based statistical and computational tools. We also present methods for mapping low resolution functional data onto the cortical surface while preserving the topological information present in the volumetric data and detail an efficient procedure for performing cross-subject, surfacebased analysis with minimal interpolation of the functional data. 1.

It is well-known that antibiotics affect commensal gut bacteria; however, only recently evidence accumulated that gut microbiota (GM) can influence the central nervous system functions. Preclinical animal studies have repeatedly highlighted the effects of antibiotics on brain activity; however, translational studies in humans are still missing. Here, we present a randomized, double-blind, placebo-controlled study investigating the effects of 7 days intake of Rifaximin (non-absorbable antibiotic) on functional brain connectivity (fc) using magnetoencephalography. Sixteen healthy volunteers were tested before and after the treatment, during resting state (rs), and during a social stressor paradigm (Cyberball game—CBG), designed to elicit feelings of exclusion. Results confirm the hypothesis of an involvement of the insular cortex as a common node of different functional networks, thus suggesting its potential role as a central mediator of cortical fc alterations, following modifications of GM. Also, the Rifaximin group displayed lower connectivity in slow and fast beta bands (15 and 25 Hz) during rest, and higher connectivity in theta (7 Hz) during the inclusion condition of the CBG, compared with controls. Altogether these results indicate a modulation of Rifaximin on frequency-specific functional connectivity that could involve cognitive flexibility and memory processing.

AFNI, SUMA, and NIML : Interprocess Communication in FMRI Data Analysis. Robert W Cox and Ziad S Saad Statistical and Scientific Computing Core National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services, USA. Linked Programs.

All data herein from Alex Martin, et al . [NIMH IRP]. Data for this presentation: AFNI_data5/ directory. Instant Analyses in AFNI and SUMA : Clusters and Correlations. AFNI “ Insta ” Functions. 3 new capabilities added to the interactive AFNI

Here we provide an example of drawing an ROI on a FreeSurfer (FS)-created surface. We turn it into a full surface dset, and also make a useful volumetric dataset from it. FS provides useful anatomical parcellations, for both surfaces and volumes + Note that we also provide volumetric versions of FS parcellations that are renumbered (for AFNI colorbar viewing) and also conveniently grouped by tissue type (WM, GM, ROI-like GM, ventricles, CSF, other); these are the *_REN_* files. + However, sometimes you want "other" ROIs, either in surface or volume You can draw ROIs conveniently on the surface, and translate them to volumes easily, potentially providing the best way to make anatomically-relevant volumetric ROIs. Open a surface with the suma GUI, and open the Draw ROI menu (ctrl+d) + You can draw in a couple different ways + Easiest (by far!) to draw on "inflated" surface" - don't get lost in sulcal/gyral patterns + Can draw more then one ROI with different string labels and index values + A four step process: - draw nearly-closed loop - click "Join" to close loop - click on surface *inside* your ROI to choose which "side" of loop is your ROI - click "Finish" to finish ROI + Can "undo" one or more times as necessary + Can save file, format will be "*.niml.roi" dset - basically a list of nodes (so you have to know which kind of mesh you drew on for later usage) - often include "lh" or "rh" in file name, for signifying particular hemisphere + There is a "run.roi2dset" script in demo to show how to: - translate *.niml.roi dset to full surface *.niml.dset dset, via program "ROI2dataset" - then translate the surface dset to volumetric (BRIK/HEAD or NII) dset, via program "3dSurf2Vol" Can view surface and/or volume ROI in SUMA and/or in AFNI, respectively + Can view separately or simultaneously! See how nicely the volumetric ROI follows brain cortex so easily + easier than drawing a volume slice-by-slice in AFNI's Draw Dataset plugin, probably, if you want an anatomical ROI. PRESENTATIONS: https://afni.nimh.nih.gov/pub/dist/edu/class_lectures/2020-03-NIH/suma/suma.pdf https://afni.nimh.nih.gov/pub/dist/edu/class_lectures/2020-03-NIH/suma/suma_keystrokes.txt -

Today was a walkthrough of the AFNI interface, and a tutorial for how to view timeseries data and model fits. Daniel started off with a sh...

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==Welcome To Q Research General== ''We hold these truths to be self-evident: that all men are created equal; that they are endowed by their Creator with certain unalienable rights; that among these are life, liberty, and the pursuit of happiness.'' '''We are researchers who deal in open-source information, reasoned argument, and dank memes. We do battle in the sphere of ideas and ideas only. We neither need nor condone the use of force in our work here.''' ==VINCIT OMNIA VERITAS====SEMPER FIDELIS====WWG1WGA== ==Q Proofs & Welcome=='''Welcome to Q Research (README FIRST, THEN PROCEED TO LURK)''' https:''//''8kun.top/qresearch/welcome.html'''THE Q MOVEMENT IS ABOUT TRUMPING THE ESTABLISHMENT''' - '''Q: The Basics - An Introduction to Q and the Great Awakening'''PDF: https:''//''8kun.top/qresearch/res/3082784.html#3082809PICS: https:''//''8kun.top/qresearch/res/3082784.html#3082821PDF & PICS Archive: >>>/comms/3196'''The Best of the Best Q Proofs''' https:''//''8kun.top/qresearch/res/4004099.html'''100+ Q Proof Graphics''' qproofs.com ==Q's Latest Posts=='''Sunday 12.29.19'''>>7653342 rt >>7653316 ———–- [Pic_insert_retry] >>7653316 —————————— Welcome to the [D] party con '''Saturday 12.28.19'''>>7645614 —————————— Easy to understand? (Cap: >>7645635)>>7643985 rt >>7643939 ———–- DNC servers not hacked>>7643917 rt >>7643883 ———–- Future will prove past>>7643842 —————————— FISA is only the beginning (Cap: >>7643898, >>7643901 pdf)>>7643289 rt >>7643247 ———–- Geo location 2015-2017?>>7643247 —————————— The only way to restore faith is through transparency and accountability. (Cap: >>7643274, >>7643313, >>7643330)>>7643055 —————————— PANIC mode (Cap: >>7643092, >>7643173)>>7640038 —————————— AG Barr talks Durham & #FISA (Cap: >>7640060)>>7639247 rt >>7639202 ———–- Post drop? 5:5? '''Friday 12.27.19'''>>7638553 —————————— They are FIGHTING for their LIVES (Cap: >>7638592)>>7638205 rt >>7637777 ———–- God Wins>>7638149 rt >>7637926 ———–- Something BIG is coming.>>7634563 —————————— Do you believe in coincidences? (Cap: >>7634583)>>7634396 —————————— Follow the money. (Cap: >>7634421) '''Monday 12.23.19'''>>7600322 —————————— Americas News room is us. (Cap: >>7600335)>>7600194 rt >>7600180 ———–- Keep up the good fight, Anons>>7600081 —————————— Nunes says anon research has aided their investigation (Caps: >>7600111)>>7599466 —————————— Why are [D]s blocking the counting of 'illegal' immigrants? (Caps: Article >>7599591, >>7599508 )>>7599338 —————————— Who really controls the [D] Party? [GS] (Caps: YT Vid >>7599388)>>7599136 —————————— POWER & CONROL (Caps: Article >>7599208, >>7599265) ==Previous Recent Q Posts=='''Sunday 12.22.19'''>>7653372'''Thursday 12.19.19'''>>7635172 '''Wednesday 12.18.19'''>>7602453 '''Q's Private Board:''' >>>/projectdcomms/ '''Q's Trip-code:''' Q !!Hs1Jq13jV6 '''Onion Link''' (access through Tor): http:''//''jthnx5wyvjvzsxtu.onion/qresearch/catalog.html ==All Q's posts==Archived at qanon.app (qanon.pub), qmap.pub, qanon.news, qposts.online ==Dealing with Clowns & Shills==New?: Use logic and reason when evaluating posts, look beyond the content of the post(s) and evaluate intent.>>7529956, >>7530061 How To Quickly Spot A Clown!

==Welcome To Q Research General== ''We hold these truths to be self-evident: that all men are created equal; that they are endowed by their Creator with certain unalienable rights; that among these are life, liberty, and the pursuit of happiness.'' '''We are researchers who deal in open-source information, reasoned argument, and dank memes. We do battle in the sphere of ideas and ideas only. We neither need nor condone the use of force in our work here.''' ==VINCIT OMNIA VERITAS====SEMPER FIDELIS====WWG1WGA== ==Q Proofs & Welcome=='''Welcome to Q Research (README FIRST, THEN PROCEED TO LURK)''' https:''//''8kun.top/qresearch/welcome.html'''THE Q MOVEMENT IS ABOUT TRUMPING THE ESTABLISHMENT''' - '''Q: The Basics - An Introduction to Q and the Great Awakening'''PDF: https:''//''8kun.top/qresearch/res/3082784.html#3082809PICS: https:''//''8kun.top/qresearch/res/3082784.html#3082821PDF & PICS Archive: >>>/comms/3196'''The Best of the Best Q Proofs''' https:''//''8kun.top/qresearch/res/4004099.html'''100+ Q Proof Graphics''' qproofs.com ==Q's Latest Posts=='''Sunday 12.29.19'''>>7653342 rt >>7653316 ———–- [Pic_insert_retry] >>7653316 —————————— Welcome to the [D] party con '''Saturday 12.28.19'''>>7645614 —————————— Easy to understand? (Cap: >>7645635)>>7643985 rt >>7643939 ———–- DNC servers not hacked>>7643917 rt >>7643883 ———–- Future will prove past>>7643842 —————————— FISA is only the beginning (Cap: >>7643898, >>7643901 pdf)>>7643289 rt >>7643247 ———–- Geo location 2015-2017?>>7643247 —————————— The only way to restore faith is through transparency and accountability. (Cap: >>7643274, >>7643313, >>7643330)>>7643055 —————————— PANIC mode (Cap: >>7643092, >>7643173)>>7640038 —————————— AG Barr talks Durham & #FISA (Cap: >>7640060)>>7639247 rt >>7639202 ———–- Post drop? 5:5? '''Friday 12.27.19'''>>7638553 —————————— They are FIGHTING for their LIVES (Cap: >>7638592)>>7638205 rt >>7637777 ———–- God Wins>>7638149 rt >>7637926 ———–- Something BIG is coming.>>7634563 —————————— Do you believe in coincidences? (Cap: >>7634583)>>7634396 —————————— Follow the money. (Cap: >>7634421) '''Monday 12.23.19'''>>7600322 —————————— Americas News room is us. (Cap: >>7600335)>>7600194 rt >>7600180 ———–- Keep up the good fight, Anons>>7600081 —————————— Nunes says anon research has aided their investigation (Caps: >>7600111)>>7599466 —————————— Why are [D]s blocking the counting of 'illegal' immigrants? (Caps: Article >>7599591, >>7599508 )>>7599338 —————————— Who really controls the [D] Party? [GS] (Caps: YT Vid >>7599388)>>7599136 —————————— POWER & CONROL (Caps: Article >>7599208, >>7599265) ==Previous Recent Q Posts=='''Sunday 12.22.19'''>>7653372'''Thursday 12.19.19'''>>7635172 '''Wednesday 12.18.19'''>>7602453 '''Q's Private Board:''' >>>/projectdcomms/ '''Q's Trip-code:''' Q !!Hs1Jq13jV6 '''Onion Link''' (access through Tor): http:''//''jthnx5wyvjvzsxtu.onion/qresearch/catalog.html ==All Q's posts==Archived at qanon.app (qanon.pub), qmap.pub, qanon.news, qposts.online ==Dealing with Clowns & Shills==New?: Use logic and reason when evaluating posts, look beyond the content of the post(s) and evaluate intent.>>7529956, >>7530061 How To Quickly Spot A Clown!

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==Welcome To Q Research General== ''We hold these truths to be self-evident: that all men are created equal; that they are endowed by their Creator with certain unalienable rights; that among these are life, liberty, and the pursuit of happiness.'' '''We are researchers who deal in open-source information, reasoned argument, and dank memes. We do battle in the sphere of ideas and ideas only. We neither need nor condone the use of force in our work here.''' ==VINCIT OMNIA VERITAS====SEMPER FIDELIS====WWG1WGA== ==Q Proofs & Welcome=='''Welcome to Q Research (README FIRST, THEN PROCEED TO LURK)''' https:''//''8kun.top/qresearch/welcome.html'''THE Q MOVEMENT IS ABOUT TRUMPING THE ESTABLISHMENT''' - '''Q: The Basics - An Introduction to Q and the Great Awakening'''PDF: https:''//''8kun.top/qresearch/res/3082784.html#3082809PICS: https:''//''8kun.top/qresearch/res/3082784.html#3082821PDF & PICS Archive: >>>/comms/3196'''The Best of the Best Q Proofs''' https:''//''8kun.top/qresearch/res/4004099.html'''100+ Q Proof Graphics''' qproofs.com ==Q's Latest Posts=='''Sunday 12.29.19'''>>7653342 rt >>7653316 ———–- [Pic_insert_retry] >>7653316 —————————— Welcome to the [D] party con '''Saturday 12.28.19'''>>7645614 —————————— Easy to understand? (Cap: >>7645635)>>7643985 rt >>7643939 ———–- DNC servers not hacked>>7643917 rt >>7643883 ———–- Future will prove past>>7643842 —————————— FISA is only the beginning (Cap: >>7643898, >>7643901 pdf)>>7643289 rt >>7643247 ———–- Geo location 2015-2017?>>7643247 —————————— The only way to restore faith is through transparency and accountability. (Cap: >>7643274, >>7643313, >>7643330)>>7643055 —————————— PANIC mode (Cap: >>7643092, >>7643173)>>7640038 —————————— AG Barr talks Durham & #FISA (Cap: >>7640060)>>7639247 rt >>7639202 ———–- Post drop? 5:5? '''Friday 12.27.19'''>>7638553 —————————— They are FIGHTING for their LIVES (Cap: >>7638592)>>7638205 rt >>7637777 ———–- God Wins>>7638149 rt >>7637926 ———–- Something BIG is coming.>>7634563 —————————— Do you believe in coincidences? (Cap: >>7634583)>>7634396 —————————— Follow the money. (Cap: >>7634421) '''Monday 12.23.19'''>>7600322 —————————— Americas News room is us. (Cap: >>7600335)>>7600194 rt >>7600180 ———–- Keep up the good fight, Anons>>7600081 —————————— Nunes says anon research has aided their investigation (Caps: >>7600111)>>7599466 —————————— Why are [D]s blocking the counting of 'illegal' immigrants? (Caps: Article >>7599591, >>7599508 )>>7599338 —————————— Who really controls the [D] Party? [GS] (Caps: YT Vid >>7599388)>>7599136 —————————— POWER & CONROL (Caps: Article >>7599208, >>7599265) ==Previous Recent Q Posts=='''Sunday 12.22.19'''>>7653372'''Thursday 12.19.19'''>>7635172 '''Wednesday 12.18.19'''>>7602453 '''Q's Private Board:''' >>>/projectdcomms/ '''Q's Trip-code:''' Q !!Hs1Jq13jV6 '''Onion Link''' (access through Tor): http:''//''jthnx5wyvjvzsxtu.onion/qresearch/catalog.html ==All Q's posts==Archived at qanon.app (qanon.pub), qmap.pub, qanon.news, qposts.online ==Dealing with Clowns & Shills==New?: Use logic and reason when evaluating posts, look beyond the content of the post(s) and evaluate intent.>>7529956, >>7530061 How To Quickly Spot A Clown!