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"),(0,r.kt)("p",null,"Although this approach was surprsingly successful, there were several major limitations to Neurosynth 1.0:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Meta-analyses were limited by ",(0,r.kt)("strong",{parentName:"p"},"concepts that can be inferred from large scale text mining")," (i.e. frequency of terms in the text).\nAlthough these features proved to be surprsingly useful for well-powered and broad cognitive constructs (e.g. 'emotion'), Neurosynth was not able\nto capture the fine-grained details of the neuroimaging literature, or allow users to define their own grouping of studies. ")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"The database is not curated, and therefore contains many ",(0,r.kt)("strong",{parentName:"p"},"inaccuracies and incomplete")," data at both the study and coordinate level.\nAside from obvious extraction erors, automated coordinate extraction lacks the ability to determine critical information, such as whether the activation is positive or negative.\nIn addition, it's not possible to segregate the coordinates into distinct contrast, conditions, or studies without manual curation.")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Coordinate-based analyses are inherently ",(0,r.kt)("strong",{parentName:"p"},"inferior to image-based")," meta-analysis, which is becoming increasingly possible with sharing of unthresholded statisical maps in repositories like ",(0,r.kt)("a",{parentName:"p",href:"https://neurovault.org/"},"NeuroVault"),"."))),(0,r.kt)("p",null,(0,r.kt)("em",{parentName:"p"},"Neurosynth Compose")," aims to address these limitations:"),(0,r.kt)("ul",null,(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Provides a web-based platform for meta-analytic neuroimaging research, allowing users to ",(0,r.kt)("strong",{parentName:"p"},"curate studies"),", and ",(0,r.kt)("strong",{parentName:"p"},"specify meta-analytic models"),". ")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},(0,r.kt)("strong",{parentName:"p"},"Flexible and easy to use"),", allowing users to perform both large-scale ",(0,r.kt)("strong",{parentName:"p"},"exploratory")," meta-analyses, as well as ",(0,r.kt)("strong",{parentName:"p"},"targeted, hypothesis-driven")," meta-analyses that conform to stringent standards such as the ","[PRISMA][https://prisma-statement.org]"," statement.")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Allows users to perfom ",(0,r.kt)("strong",{parentName:"p"},"image-based meta-analysis")," using unthresholded images from NeuroVault (in progress).")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Quick, reproducible and transparent ",(0,r.kt)("strong",{parentName:"p"},"sharing of results"),".")),(0,r.kt)("li",{parentName:"ul"},(0,r.kt)("p",{parentName:"li"},"Incentivizes ",(0,r.kt)("strong",{parentName:"p"},"collaborative curation")," of neuroimaging studies in a accesible ",(0,r.kt)("strong",{parentName:"p"},"centralized repository")," (NeuroStore, see below)."))),(0,r.kt)("h2",{id:"neurostore"},"NeuroStore"),(0,r.kt)("p",null,"NeuroStore is the centralized repository for neuroimaging data amenable to meta-analysis, including coordinates, images, and metadata.\nNeuroStore serves as the data backend for Neurosynth Compose, but is also designed to be a standalone interoperable resource for the neuroimaging community."),(0,r.kt)("p",null,"NeuroStore ingests data from a number of sources, including NeuroVault, NeuroQuery, and Neurosynth (ACE), and provides a unified API for querying the database."),(0,r.kt)("p",null,"Importantly, data on NeuroStore can be ",(0,r.kt)("strong",{parentName:"p"},"curated")," the community, allowing users to correct errors in coordinate extraction, and add new studies and coordinates. 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"),(0,i.kt)("p",null,"At the end of the process, you will be ready to create a ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/guide/glossary#studyset"},(0,i.kt)("strong",{parentName:"a"},"Studyset"))," of related studies that are amenable for neuroimaging meta-analysis"),(0,i.kt)("h2",{id:"getting-started"},"Getting Started"),(0,i.kt)("p",null,"The curation interface uses columns as a way to label studies based on their current status.\nThe left most column is the starting point and all studies imported into the project will begin there.\nThe right most column is the ",(0,i.kt)("strong",{parentName:"p"},"inclusion column")," and is the place where studies will go to be included in the meta-analysis. "),(0,i.kt)("p",null,'The goal is to get studies from the left most starting column, and narrow them down to a final subset of included studies in the right most column.\nIf a study is not eligible for inclusion at any point, it should be marked as "excluded" before reaching the inclusion column.'),(0,i.kt)("p",null,"The curation step is complete when all studies have been categorized, either by being included or excluded."),(0,i.kt)("p",null,"When you first begin ",(0,i.kt)("em",{parentName:"p"},"Curation"),", you will choose between different workflows, which vary in how rigorous or systematic the selection of studies will be."),(0,i.kt)("admonition",{title:"How specific to be?",type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"Performing a systematic meta-analysis involves a substantial amount of effort. It is up to you, the researcher, how rigorous to be in this process. We reccomend thinking about your ",(0,i.kt)("em",{parentName:"p"},"goals")," prior to starting this process so that you can have clear inclusion guidelines. If you are looking for an exploratory analysis, we reccomend following the tutorial for ",(0,i.kt)("em",{parentName:"p"},"automated meta-analysis"),", which replaces manual curation with an automated selection of studies. Note that automated meta-analyses are not a replacement for a careful systematic meta-analysis.")),(0,i.kt)("h3",{id:"prisma-workflow"},"PRISMA Workflow"),(0,i.kt)("p",null,"PRISMA stands for the ",(0,i.kt)("strong",{parentName:"p"},"Preferred Reporting Items for Systematic Review and Meta-Analyses"),". The\n",(0,i.kt)("a",{parentName:"p",href:"http://www.prisma-statement.org/?AspxAutoDetectCookieSupport=1"},"PRISMA guidelines")," are a set of rules for reporting a\nsystematic review, and are the gold standard for producing a proper, rigorous, and transparent meta-analysis."),(0,i.kt)("p",null,"If you are trying to create a rigorous ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/manual"},"manual meta-analysis"),", or if you are trying to create a\n",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/semi-automated"},"PRISMA compliant semi-automated meta-analysis"),", you will want to select this option."),(0,i.kt)("p",null,"When you select this option, neurosynth-compose will automatically initialize the curation step with 4 distinct columns as\ndictated by PRISMA guidelines: ",(0,i.kt)("strong",{parentName:"p"},"Identification, Screening, Eligibility, Included"),"."),(0,i.kt)("p",null,"After importing studies into neurosynth, they will be placed into the identification column and studies are triaged from there."),(0,i.kt)("admonition",{title:"PRISMA Summary",type:"info"},(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Identification")," column is where all imported studies are deposited into initially. As alluded to by the name, the identification\ncolumn is where you identify all records yielded from your search. In this column, you wil exclude studies purely based on whether they are\nduplicates of existing studies. All other studies are promoted."),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Screening")," column consists of all records that have been screened for duplicates. In this column, you want to review the titles/abstracts of studies\nand exclude purely based on whether they are irrelevant to your research question or domain. All other studies are promoted. "),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Eligibility")," column consists of all records that have been screened for duplicates and irrelevant content. In this column, you want to\nreview the full text of studies and exclude based on whether the study described aligns with the standards of the meta-analysis itself. Reasons\nfor exclusion may include wrong setting, wrong patient population, wrong intervention, wrong paragdigm, etc."),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Included")," column consists of all records that have passed previous levels of exclusion and can be considered for the next step of the project."),(0,i.kt)("p",{parentName:"admonition"},"For more information, consult the ",(0,i.kt)("a",{parentName:"p",href:"http://www.prisma-statement.org/?AspxAutoDetectCookieSupport=1"},"PRISMA guidelines"),".")),(0,i.kt)("h3",{id:"simple-workflow"},"Simple Workflow"),(0,i.kt)("p",null,"If you want to create a ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/semi-automated"},"semi-automated meta-analysis")," (i.e. perform manual review on a large-scale study search), you'll want to select this option."),(0,i.kt)("p",null,"This workflow is initalized with only two columns. As before, the left most column is where studies will be placed when they are imported. However, unlike a full PRISMA workflow, all exclusion occurs in this column. All studies not excluded are then promoted to the right most column for inclusion into the meta-analysis."),(0,i.kt)("h2",{id:"importing"},"Importing"),(0,i.kt)("p",null,"To begin importing studies into your project clicking the ",(0,i.kt)("strong",{parentName:"p"},"IMPORT STUDIES")," button."),(0,i.kt)("p",null,"You will be asked to choose a source, name your import, and address\nany potential duplicate studies."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"We recommend giving each import a meaningful name. This will be useful when you come back\nand want to know where a certain study was imported from.")),(0,i.kt)("h3",{id:"import-from-neurostore"},"Import from Neurostore"),(0,i.kt)("p",null,"Neurostore indexes a large number of neuroimaging studies which are ready for meta-analysis. Studies in Neurostore have been pre-processed, including extracting peak activation coordinates from Tables in the text, and computing semantic features from the abstract/full text. Neurostore also indexes studies which other users have annotated and made available to others for re-use."),(0,i.kt)("p",null,"Importing from Neurostore utilizes the Study search UI similar to the ",(0,i.kt)("a",{parentName:"p",href:"https://compose.neurosynth.org/studies"},"Study Page"),".\nAfter entering your search, click the bottom right button to import the searched studies into your project."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"Importing from Neurostore can save you a lot of time, as these studies are much more likely to be amenable to meta-analysis, and have pre-extracted coordinates. However, note that some manual annotation may still be required to verify the coordinate extraction, and choose the relevant Analysis (i.e. contrast) for final inclusion.")),(0,i.kt)("h3",{id:"import-from-pubmed"},"Import from PubMed"),(0,i.kt)("p",null,"Use this option to import studies directly from PubMed. To start, you need to go to the ",(0,i.kt)("a",{parentName:"p",href:"https://pubmed.ncbi.nlm.nih.gov/"},"PubMed Site"),"\nand either enter in a search or navigate to a previously created collection. "),(0,i.kt)("p",null,"To import the search or collection from PubMed into neurosynth-compose, you will need a text file containing a list of PMIDs.\nYou can obtain this by going to your collection/search and clicking the ",(0,i.kt)("strong",{parentName:"p"},"Save")," button. Set ",(0,i.kt)("strong",{parentName:"p"},"Selection")," to ",(0,i.kt)("strong",{parentName:"p"},"All results"),"\nand set ",(0,i.kt)("strong",{parentName:"p"},"Format")," to ",(0,i.kt)("strong",{parentName:"p"},"PMID"),". Click ",(0,i.kt)("strong",{parentName:"p"},"Create file")," and your text file containing the PMIDs will be generated and downloaded."),(0,i.kt)("admonition",{type:"caution"},(0,i.kt)("p",{parentName:"admonition"},"Neurosynth-Compose uses the PubMed API to import studies. As a result, the maximum number of PMIDs that can be imported at once is 1,500.\nIf your collection has more than 1,500 PMIDs, split the import into multiple files.")),(0,i.kt)("h3",{id:"import-from-bibtexrisendnote"},"Import from BibTex/RIS/endnote"),(0,i.kt)("p",null,"Use this option to import studies via a .bib, .RIS, or .enw file. 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If a study is marked as a duplicate, it is marked as ",(0,i.kt)("strong",{parentName:"p"},"excluded")," but it is not discarded to ensure complete provenance. ")),(0,i.kt)("p",null,"There are two potential ways that duplicates can occur:"),(0,i.kt)("h4",{id:"duplicates-are-detected-between-the-studies-being-imported-and-the-studies-already-in-the-project"},"Duplicates are detected between the studies being imported and the studies already in the project"),(0,i.kt)("p",null,"If any study being important has the same title, PMID, or DOI is the same as\none already in the project, you will be asked reconcile these duplicates."),(0,i.kt)("p",null,'Note that if you mark a study that is already promoted as a duplicate, it will be "demoted" back to the first column and marked as "duplicate". It is reccomended to mark as duplicate the incoming study to avoid this. '),(0,i.kt)("h4",{id:"duplicates-are-detected-within-the-file-you-are-importing"},"Duplicates are detected within the file you are importing"),(0,i.kt)("p",null,"Although rare, it is possible to have duplicates within a given import. For example, if within a RIS file there are duplicate entries. In this case, you will be asked to select which study to keep. Studies marked as duplicates will still be imported but marked as excluded. "),(0,i.kt)("h2",{id:"excluding-and-promoting-studies"},"Excluding and Promoting Studies"),(0,i.kt)("p",null,"Once studies have been imported into the first column of the curation phase, they need to be reviewed for inclusion into your meta-analysis.\nAll studies must be either excluded or moved to the inclusion column in order to progress to the extraction phase."),(0,i.kt)("p",null,"To begin, either click on the button at the top of the column or click on any study in the column. This will open up a page which will show the study\nalong with the following options: ",(0,i.kt)("strong",{parentName:"p"},"PROMOTE, NEEDS REVIEW"),", and ",(0,i.kt)("strong",{parentName:"p"},"EXCLUDE"),". There is also a button to ",(0,i.kt)("strong",{parentName:"p"},"ADD TAGS")," which will assign an informational tag to the study."),(0,i.kt)("h3",{id:"exclude"},"Exclude"),(0,i.kt)("p",null,"To exclude a study, click the ",(0,i.kt)("strong",{parentName:"p"},"EXCLUDE")," button and select the exclusion reason. You can either choose from the preset exclusion reasons or you can begin\ntyping to create a new one."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"For the PRISMA workflow, the default exclusion reason wil depend on the phase you are in (identification vs screening vs eligibility), to match the PRISMA guidelines. While we do not recommend it, you can click the arrow button and start typing in the input to create a new exclusion reason.\nRevisit the ",(0,i.kt)("a",{parentName:"p",href:"./Curation#prisma-workflow"},"PRISMA workflow")," to review reccomended exclusion criteria.")),(0,i.kt)("h3",{id:"promote"},"Promote"),(0,i.kt)("p",null,"If a study meets inclusion critera (for the current phase), click ",(0,i.kt)("strong",{parentName:"p"},"PROMOTE")," to move the study forward to the next curation column. If it is moved into the right most inclusion column, then it will be included in the meta-analysis."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"For the first column (especially in a PRISMA workflow) it can be tedious to promote non-duplicates to the next column. If all duplicates have been resolved, you can exit the dialog and click ",(0,i.kt)("strong",{parentName:"p"},"PROMOTE ALL UNCATEGORIZED STUDIES")," to advance all non-duplicate studies to the next column.")),(0,i.kt)("h2",{id:"on-to-extraction"},"On to Extraction"),(0,i.kt)("p",null,"When you have categorized all imported studies by either excluding them or moving them to the inclusion column, then you have\nsuccessfully completed the curation portion of the meta-analysis."),(0,i.kt)("p",null,(0,i.kt)("em",{parentName:"p"},"Neurosynth Compose")," will detect this and reveal a new button: ",(0,i.kt)("strong",{parentName:"p"},"MOVE TO EXTRACTION PHASE"),". 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"),(0,i.kt)("p",null,"At the end of the process, you will be ready to create a ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/guide/glossary#studyset"},(0,i.kt)("strong",{parentName:"a"},"Studyset"))," of related studies that are amenable for neuroimaging meta-analysis"),(0,i.kt)("h2",{id:"getting-started"},"Getting Started"),(0,i.kt)("p",null,"The curation interface uses columns as a way to label studies based on their current status.\nThe left most column is the starting point and all studies imported into the project will begin there.\nThe right most column is the ",(0,i.kt)("strong",{parentName:"p"},"inclusion column")," and is the place where studies will go to be included in the meta-analysis. "),(0,i.kt)("p",null,'The goal is to get studies from the left most starting column, and narrow them down to a final subset of included studies in the right most column.\nIf a study is not eligible for inclusion at any point, it should be marked as "excluded" before reaching the inclusion column.'),(0,i.kt)("p",null,"The curation step is complete when all studies have been categorized, either by being included or excluded."),(0,i.kt)("p",null,"When you first begin ",(0,i.kt)("em",{parentName:"p"},"Curation"),", you will choose between different workflows, which vary in how rigorous or systematic the selection of studies will be."),(0,i.kt)("admonition",{title:"How specific to be?",type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"Performing a systematic meta-analysis involves a substantial amount of effort. It is up to you, the researcher, how rigorous to be in this process. 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The\n",(0,i.kt)("a",{parentName:"p",href:"http://www.prisma-statement.org/?AspxAutoDetectCookieSupport=1"},"PRISMA guidelines")," are a set of rules for reporting a\nsystematic review, and are the gold standard for producing a proper, rigorous, and transparent meta-analysis."),(0,i.kt)("p",null,"If you are trying to create a rigorous ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/manual"},"manual meta-analysis"),", or if you are trying to create a\n",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/semi-automated"},"PRISMA compliant semi-automated meta-analysis"),", you will want to select this option."),(0,i.kt)("p",null,"When you select this option, neurosynth-compose will automatically initialize the curation step with 4 distinct columns as\ndictated by PRISMA guidelines: ",(0,i.kt)("strong",{parentName:"p"},"Identification, Screening, Eligibility, Included"),"."),(0,i.kt)("p",null,"After importing studies into neurosynth, they will be placed into the identification column and studies are triaged from there."),(0,i.kt)("admonition",{title:"PRISMA Summary",type:"info"},(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Identification")," column is where all imported studies are deposited into initially. As alluded to by the name, the identification\ncolumn is where you identify all records yielded from your search. In this column, you wil exclude studies purely based on whether they are\nduplicates of existing studies. All other studies are promoted."),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Screening")," column consists of all records that have been screened for duplicates. In this column, you want to review the titles/abstracts of studies\nand exclude purely based on whether they are irrelevant to your research question or domain. All other studies are promoted. "),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Eligibility")," column consists of all records that have been screened for duplicates and irrelevant content. In this column, you want to\nreview the full text of studies and exclude based on whether the study described aligns with the standards of the meta-analysis itself. Reasons\nfor exclusion may include wrong setting, wrong patient population, wrong intervention, wrong paragdigm, etc."),(0,i.kt)("p",{parentName:"admonition"},"The ",(0,i.kt)("strong",{parentName:"p"},"Included")," column consists of all records that have passed previous levels of exclusion and can be considered for the next step of the project."),(0,i.kt)("p",{parentName:"admonition"},"For more information, consult the ",(0,i.kt)("a",{parentName:"p",href:"http://www.prisma-statement.org/?AspxAutoDetectCookieSupport=1"},"PRISMA guidelines"),".")),(0,i.kt)("h3",{id:"simple-workflow"},"Simple Workflow"),(0,i.kt)("p",null,"If you want to create a ",(0,i.kt)("a",{parentName:"p",href:"/compose-docs/tutorial/semi-automated"},"semi-automated meta-analysis")," (i.e. perform manual review on a large-scale study search), you'll want to select this option."),(0,i.kt)("p",null,"This workflow is initalized with only two columns. As before, the left most column is where studies will be placed when they are imported. However, unlike a full PRISMA workflow, all exclusion occurs in this column. All studies not excluded are then promoted to the right most column for inclusion into the meta-analysis."),(0,i.kt)("h2",{id:"importing"},"Importing"),(0,i.kt)("p",null,"To begin importing studies into your project clicking the ",(0,i.kt)("strong",{parentName:"p"},"IMPORT STUDIES")," button."),(0,i.kt)("p",null,"You will be asked to choose a source, name your import, and address\nany potential duplicate studies."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"We recommend giving each import a meaningful name. This will be useful when you come back\nand want to know where a certain study was imported from.")),(0,i.kt)("h3",{id:"import-from-neurostore"},"Import from Neurostore"),(0,i.kt)("p",null,"Neurostore indexes a large number of neuroimaging studies which are ready for meta-analysis. Studies in Neurostore have been pre-processed, including extracting peak activation coordinates from Tables in the text, and computing semantic features from the abstract/full text. Neurostore also indexes studies which other users have annotated and made available to others for re-use."),(0,i.kt)("p",null,"Importing from Neurostore utilizes the Study search UI similar to the ",(0,i.kt)("a",{parentName:"p",href:"https://compose.neurosynth.org/studies"},"Study Page"),".\nAfter entering your search, click the bottom right button to import the searched studies into your project."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"Importing from Neurostore can save you a lot of time, as these studies are much more likely to be amenable to meta-analysis, and have pre-extracted coordinates. However, note that some manual annotation may still be required to verify the coordinate extraction, and choose the relevant Analysis (i.e. contrast) for final inclusion.")),(0,i.kt)("h3",{id:"import-from-pubmed"},"Import from PubMed"),(0,i.kt)("p",null,"Use this option to import studies directly from PubMed. To start, you need to go to the ",(0,i.kt)("a",{parentName:"p",href:"https://pubmed.ncbi.nlm.nih.gov/"},"PubMed Site"),"\nand either enter in a search or navigate to a previously created collection. "),(0,i.kt)("p",null,"To import the search or collection from PubMed into neurosynth-compose, you will need a text file containing a list of PMIDs.\nYou can obtain this by going to your collection/search and clicking the ",(0,i.kt)("strong",{parentName:"p"},"Save")," button. Set ",(0,i.kt)("strong",{parentName:"p"},"Selection")," to ",(0,i.kt)("strong",{parentName:"p"},"All results"),"\nand set ",(0,i.kt)("strong",{parentName:"p"},"Format")," to ",(0,i.kt)("strong",{parentName:"p"},"PMID"),". Click ",(0,i.kt)("strong",{parentName:"p"},"Create file")," and your text file containing the PMIDs will be generated and downloaded."),(0,i.kt)("admonition",{type:"caution"},(0,i.kt)("p",{parentName:"admonition"},"Neurosynth-Compose uses the PubMed API to import studies. As a result, the maximum number of PMIDs that can be imported at once is 1,500.\nIf your collection has more than 1,500 PMIDs, split the import into multiple files.")),(0,i.kt)("h3",{id:"import-from-bibtexrisendnote"},"Import from BibTex/RIS/endnote"),(0,i.kt)("p",null,"Use this option to import studies via a .bib, .RIS, or .enw file. This may be useful if you want to import from a citation manager like Zotero."),(0,i.kt)("h3",{id:"custom-studies"},"Custom Studies"),(0,i.kt)("p",null,"If there is any record that cannot be easily imported using one of the methods listed above, you can also manually create a study. This may be necessary\nto include resources like unpublished studies."),(0,i.kt)("h3",{id:"duplicates"},"Duplicates"),(0,i.kt)("p",null,'If duplicates are detected in your import, you will be asked how to re-concile them by choosing which of the studies to keep by choosing "KEEP THIS STUDY". Matching duplicates will be automatically marked for exclusion. Note that as a user, you can over-ride any of these selection at any time, and choose which studies to keep or exclude. '),(0,i.kt)("admonition",{type:"info"},(0,i.kt)("p",{parentName:"admonition"},(0,i.kt)("em",{parentName:"p"},"Neurosynth Compose")," does not delete studies. If a study is marked as a duplicate, it is marked as ",(0,i.kt)("strong",{parentName:"p"},"excluded")," but it is not discarded to ensure complete provenance. ")),(0,i.kt)("p",null,"There are two potential ways that duplicates can occur:"),(0,i.kt)("h4",{id:"duplicates-are-detected-between-the-studies-being-imported-and-the-studies-already-in-the-project"},"Duplicates are detected between the studies being imported and the studies already in the project"),(0,i.kt)("p",null,"If any study being important has the same title, PMID, or DOI is the same as\none already in the project, you will be asked reconcile these duplicates."),(0,i.kt)("p",null,'Note that if you mark a study that is already promoted as a duplicate, it will be "demoted" back to the first column and marked as "duplicate". It is reccomended to mark as duplicate the incoming study to avoid this. '),(0,i.kt)("h4",{id:"duplicates-are-detected-within-the-file-you-are-importing"},"Duplicates are detected within the file you are importing"),(0,i.kt)("p",null,"Although rare, it is possible to have duplicates within a given import. For example, if within a RIS file there are duplicate entries. In this case, you will be asked to select which study to keep. Studies marked as duplicates will still be imported but marked as excluded. "),(0,i.kt)("h2",{id:"excluding-and-promoting-studies"},"Excluding and Promoting Studies"),(0,i.kt)("p",null,"Once studies have been imported into the first column of the curation phase, they need to be reviewed for inclusion into your meta-analysis.\nAll studies must be either excluded or moved to the inclusion column in order to progress to the extraction phase."),(0,i.kt)("p",null,"To begin, either click on the button at the top of the column or click on any study in the column. This will open up a page which will show the study\nalong with the following options: ",(0,i.kt)("strong",{parentName:"p"},"PROMOTE, NEEDS REVIEW"),", and ",(0,i.kt)("strong",{parentName:"p"},"EXCLUDE"),". There is also a button to ",(0,i.kt)("strong",{parentName:"p"},"ADD TAGS")," which will assign an informational tag to the study."),(0,i.kt)("h3",{id:"exclude"},"Exclude"),(0,i.kt)("p",null,"To exclude a study, click the ",(0,i.kt)("strong",{parentName:"p"},"EXCLUDE")," button and select the exclusion reason. You can either choose from the preset exclusion reasons or you can begin\ntyping to create a new one."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"For the PRISMA workflow, the default exclusion reason wil depend on the phase you are in (identification vs screening vs eligibility), to match the PRISMA guidelines. While we do not recommend it, you can click the arrow button and start typing in the input to create a new exclusion reason.\nRevisit the ",(0,i.kt)("a",{parentName:"p",href:"./Curation#prisma-workflow"},"PRISMA workflow")," to review reccomended exclusion criteria.")),(0,i.kt)("h3",{id:"promote"},"Promote"),(0,i.kt)("p",null,"If a study meets inclusion critera (for the current phase), click ",(0,i.kt)("strong",{parentName:"p"},"PROMOTE")," to move the study forward to the next curation column. If it is moved into the right most inclusion column, then it will be included in the meta-analysis."),(0,i.kt)("admonition",{type:"tip"},(0,i.kt)("p",{parentName:"admonition"},"For the first column (especially in a PRISMA workflow) it can be tedious to promote non-duplicates to the next column. 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- + \ No newline at end of file diff --git a/blog/archive.html b/blog/archive.html index 73a11bf..44d55aa 100644 --- a/blog/archive.html +++ b/blog/archive.html @@ -5,13 +5,13 @@ Archive | Neurosynth Compose Docs - +
- + \ No newline at end of file diff --git a/blog/first-blog-post.html b/blog/first-blog-post.html index 6a9ecd7..c3e57a3 100644 --- a/blog/first-blog-post.html +++ b/blog/first-blog-post.html @@ -5,13 +5,13 @@ First Blog Post | Neurosynth Compose Docs - +
- + \ No newline at end of file diff --git a/blog/tags.html b/blog/tags.html index 8403426..f3f05d7 100644 --- a/blog/tags.html +++ b/blog/tags.html @@ -5,13 +5,13 @@ Tags | Neurosynth Compose Docs - +
- + \ No newline at end of file diff --git a/blog/tags/hello.html b/blog/tags/hello.html index 55c8f26..3605621 100644 --- a/blog/tags/hello.html +++ b/blog/tags/hello.html @@ -5,13 +5,13 @@ One post tagged with "hello" | Neurosynth Compose Docs - +

One post tagged with "hello"

View All Tags
- + \ No newline at end of file diff --git a/blog/tags/neurosynth.html b/blog/tags/neurosynth.html index 2f10649..03fae6d 100644 --- a/blog/tags/neurosynth.html +++ b/blog/tags/neurosynth.html @@ -5,13 +5,13 @@ One post tagged with "neurosynth" | Neurosynth Compose Docs - +

One post tagged with "neurosynth"

View All Tags
- + \ No newline at end of file diff --git a/guide.html b/guide.html index 98add9f..9881e4e 100644 --- a/guide.html +++ b/guide.html @@ -5,13 +5,13 @@ User Guide | Neurosynth Compose Docs - +
-
- +
+ \ No newline at end of file diff --git a/guide/glossary.html b/guide/glossary.html index a688290..33f3bae 100644 --- a/guide/glossary.html +++ b/guide/glossary.html @@ -5,7 +5,7 @@ Glossary | Neurosynth Compose Docs - + @@ -28,8 +28,8 @@ The contents of an analysis include the terms applied to the groups/conditions and their respective weights in the contrast. An analysis also contains the results of the statistical contrast either with an image and/or a table -indicating significant results

Condition​

Overview​

A condition is term/word that represents a psychological (e.g., 2-back), physical (e.g., biking)

Weights​

Point​

Overview​

Image​

- +indicating significant results

Condition​

Overview​

A condition is term/word that represents a psychological (e.g., 2-back), physical (e.g., biking)

Weights​

Point​

Overview​

Image​

+ \ No newline at end of file diff --git a/guide/walkthrough.html b/guide/walkthrough.html index 286a6b1..ac757f8 100644 --- a/guide/walkthrough.html +++ b/guide/walkthrough.html @@ -5,13 +5,13 @@ Walkthrough | Neurosynth Compose Docs - +
-
- +
+ \ No newline at end of file diff --git a/guide/walkthrough/Project.html b/guide/walkthrough/Project.html index 2a02caf..559c40c 100644 --- a/guide/walkthrough/Project.html +++ b/guide/walkthrough/Project.html @@ -5,7 +5,7 @@ Project | Neurosynth Compose Docs - + @@ -13,8 +13,8 @@

Project

A project organizes the the various steps needed to create a meta-analysis from start to finish.

Within a project you will be able to:

  1. Curate studies of interest and select the ones to be included in the meta-analysis
  2. Extract the relevant data such as activation coordinates and other meta-data
  3. Specify the algorithm and corrector you would like to use
  4. Run the meta-analysis and View the results

In each project, you can define a define a single StudySe (i.e. a collection of related studies), and one or more MetaAnalysis specifications.

You can open a specific project by logging in, navigating to the My Projects page, and selecting a project you've created.

When you view a project for the first time, you'll notice that you'll default to the "Edit Project" tab. The "View Meta-Analyses" tab will be disabled and will become enabled when you have created the first meta-analysis specification -for the project.

- +for the project.

+ \ No newline at end of file diff --git a/guide/walkthrough/Project/Curation.html b/guide/walkthrough/Project/Curation.html index 94055fe..9a76cf3 100644 --- a/guide/walkthrough/Project/Curation.html +++ b/guide/walkthrough/Project/Curation.html @@ -5,7 +5,7 @@ Curation | Neurosynth Compose Docs - + @@ -36,8 +36,8 @@ along with the following options: PROMOTE, NEEDS REVIEW, and EXCLUDE. There is also a button to ADD TAGS which will assign an informational tag to the study.

Exclude​

To exclude a study, click the EXCLUDE button and select the exclusion reason. You can either choose from the preset exclusion reasons or you can begin typing to create a new one.

tip

For the PRISMA workflow, the default exclusion reason wil depend on the phase you are in (identification vs screening vs eligibility), to match the PRISMA guidelines. While we do not recommend it, you can click the arrow button and start typing in the input to create a new exclusion reason. Revisit the PRISMA workflow to review reccomended exclusion criteria.

Promote​

If a study meets inclusion critera (for the current phase), click PROMOTE to move the study forward to the next curation column. If it is moved into the right most inclusion column, then it will be included in the meta-analysis.

tip

For the first column (especially in a PRISMA workflow) it can be tedious to promote non-duplicates to the next column. If all duplicates have been resolved, you can exit the dialog and click PROMOTE ALL UNCATEGORIZED STUDIES to advance all non-duplicate studies to the next column.

On to Extraction​

When you have categorized all imported studies by either excluding them or moving them to the inclusion column, then you have -successfully completed the curation portion of the meta-analysis.

Neurosynth Compose will detect this and reveal a new button: MOVE TO EXTRACTION PHASE. This will move you back to the project page and get you started on the next major component to building your meta-analysis: extraction.

- +successfully completed the curation portion of the meta-analysis.

Neurosynth Compose will detect this and reveal a new button: MOVE TO EXTRACTION PHASE. This will move you back to the project page and get you started on the next major component to building your meta-analysis: extraction.

+ \ No newline at end of file diff --git a/guide/walkthrough/Project/Extraction.html b/guide/walkthrough/Project/Extraction.html index bc2fecc..c0f083b 100644 --- a/guide/walkthrough/Project/Extraction.html +++ b/guide/walkthrough/Project/Extraction.html @@ -5,7 +5,7 @@ Extraction | Neurosynth Compose Docs - + @@ -24,8 +24,8 @@ are imported into the curation phase are excluded during the curation process. Inserting these studies into the database would clutter it and create a lot of empty entries which don't have coordinates and might not even be used. By waiting until we have our finalized included subset of studies, we reduce the number of empty, useless studies in the database.

Annotations​

Study Editing​

Studies in the extraction phase are filtered and categorized to help better organize and facilitate the process. Initially, all studies -start as Uncategorized. The user can then decide to mark them as Save For Later if they want to revisit the study, or Completed.

Read Only Studies​

Study Annotations​

Study Edit Interface​

Syncing Between Curation and Extraction​

- +start as Uncategorized. The user can then decide to mark them as Save For Later if they want to revisit the study, or Completed.

Read Only Studies​

Study Annotations​

Study Edit Interface​

Syncing Between Curation and Extraction​

+ \ No newline at end of file diff --git a/guide/walkthrough/Project/Specification.html b/guide/walkthrough/Project/Specification.html index 2a27697..635e562 100644 --- a/guide/walkthrough/Project/Specification.html +++ b/guide/walkthrough/Project/Specification.html @@ -5,13 +5,13 @@ Specification | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/guide/walkthrough/Studies.html b/guide/walkthrough/Studies.html index 7db6d21..cbe1141 100644 --- a/guide/walkthrough/Studies.html +++ b/guide/walkthrough/Studies.html @@ -5,13 +5,13 @@ Studies Page | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/guide/walkthrough/Studies/Searching.html b/guide/walkthrough/Studies/Searching.html index 067febd..584157f 100644 --- a/guide/walkthrough/Studies/Searching.html +++ b/guide/walkthrough/Studies/Searching.html @@ -5,7 +5,7 @@ Searching | Neurosynth Compose Docs - + @@ -15,8 +15,8 @@ certain AND or NOT operators amongst multiple clauses.

For example, consider the search: nicotine OR smoking -marijuana. In this example, the search results returned to you will be all the results yielded from nicotine unioned with all the results of smoking -marijuana. Having -marijuana here does not relate to the entire search term - just smoking.

To ensure that you do not have any mention of marijuana in your returned papers, you must search: nicotine -marijuana or smoking -marijuana.

The same case applies for AND operations. In general, OR unions between various search groups consisting of and, not, and quoted search terms.

Study Data Type​

Studies can either report their findings as coordinate data, image data, or in some cases, both. Using the Study Data Type button, you can filter the results so that only coordinate or image data appears. For example, if you are doing a coordinate based meta-analysis, you -will want to filter the results to show only studies that report coordinates.

Sorting Results​

Use the Sort By feature to sort the results based on a given property. You can also set this to be ascending or descending.

Filtering​

To filter the results of the search, click on the orange Add Filter button. You have the option of filtering by title, description, author, or publication. Enter the string you want to filter by and click add to apply the filter.

Only one filter can be applied for each field. In order to remove a filter, simply click on the delete button on the given filter.

- +will want to filter the results to show only studies that report coordinates.

Sorting Results​

Use the Sort By feature to sort the results based on a given property. You can also set this to be ascending or descending.

Filtering​

To filter the results of the search, click on the orange Add Filter button. You have the option of filtering by title, description, author, or publication. Enter the string you want to filter by and click add to apply the filter.

Only one filter can be applied for each field. In order to remove a filter, simply click on the delete button on the given filter.

+ \ No newline at end of file diff --git a/guide/walkthrough/meta-analyses.html b/guide/walkthrough/meta-analyses.html index f1b6dac..b057e31 100644 --- a/guide/walkthrough/meta-analyses.html +++ b/guide/walkthrough/meta-analyses.html @@ -5,13 +5,13 @@ Meta-Analyses Page | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/guide/walkthrough/search.html b/guide/walkthrough/search.html index 3841b54..8985982 100644 --- a/guide/walkthrough/search.html +++ b/guide/walkthrough/search.html @@ -5,13 +5,13 @@ Searching | Neurosynth Compose Docs - +
-

Intro To Searching

Searching Studies​

Neurosynth-Compose supports multiple ways to search for studies.

Searching Studysets​

Searching Meta-Analyses​

- +

Intro To Searching

Searching Studies​

Neurosynth-Compose supports multiple ways to search for studies.

Searching Studysets​

Searching Meta-Analyses​

+ \ No newline at end of file diff --git a/guide/walkthrough/studysets.html b/guide/walkthrough/studysets.html index 269b227..1759519 100644 --- a/guide/walkthrough/studysets.html +++ b/guide/walkthrough/studysets.html @@ -5,13 +5,13 @@ Studysets Page | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/index.html b/index.html index c8d9d26..12c395d 100644 --- a/index.html +++ b/index.html @@ -5,13 +5,13 @@ What is Neurosynth Compose? | Neurosynth Compose Docs - +
-

What is Neurosynth Compose?

Neurosynth Compose is the next-generation of Neurosynth, enabling users to easily perform custom neuroimaging meta-analyses using a fully web-based platform, with no programming experience required.

Neurosynth Compose is free to use and helps users:

  • 🔎 Search across over 15,000 studies in the Neurosynth database, or import from external databasets such as PubMed.
  • 🗃️ Curate your StudySet using systematic review tools conforming to the PRISMA guidelines.
  • 📝 Extract coordinates and metadata for each study, leveraging thousands of pre-extracted studies to minimize effort.
  • 📊 Analyze by specfying a reproducible NiMARE workflow, and execute it locally or in the cloud.
  • 🔗 Share with the community with complete provenance and reproducibility.

Get started! 🚀​

Tutorials

Tutorials show you how to use Neurosynth Compose with complete end-to-end examples.

Go to Tutorials

User Guide

The User Guide provides a detailed overview of the platform, and explains key concepts and features.

Go to User Guide

Getting Help​

  • Ask a question on Neurostars using the neurosynth-compose tag.
  • Report a bug or request a feature on GitHub
  • Help us improve the platform by using the feedback button in the bottom right corner of the page.
- +

What is Neurosynth Compose?

Neurosynth Compose is the next-generation of Neurosynth, enabling users to easily perform custom neuroimaging meta-analyses using a fully web-based platform, with no programming experience required.

Neurosynth Compose is free to use and helps users:

  • 🔎 Search across over 15,000 studies in the Neurosynth database, or import from external databasets such as PubMed.
  • 🗃️ Curate your StudySet using systematic review tools conforming to the PRISMA guidelines.
  • 📝 Extract coordinates and metadata for each study, leveraging thousands of pre-extracted studies to minimize effort.
  • 📊 Analyze by specfying a reproducible NiMARE workflow, and execute it locally or in the cloud.
  • 🔗 Share with the community with complete provenance and reproducibility.

Get started! 🚀​

Tutorials

Tutorials show you how to use Neurosynth Compose with complete end-to-end examples.

Go to Tutorials

User Guide

The User Guide provides a detailed overview of the platform, and explains key concepts and features.

Go to User Guide

Getting Help​

  • Ask a question on Neurostars using the neurosynth-compose tag.
  • Report a bug or request a feature on GitHub
  • Help us improve the platform by using the feedback button in the bottom right corner of the page.
+ \ No newline at end of file diff --git a/introduction/ecosystem.html b/introduction/ecosystem.html index f764be2..02ac777 100644 --- a/introduction/ecosystem.html +++ b/introduction/ecosystem.html @@ -5,7 +5,7 @@ Ecosystem for fMRI Meta-Analysis | Neurosynth Compose Docs - + @@ -28,8 +28,8 @@ Additionally, the NeuroQuery database will feed directly into NeuroStore as a source of coordinates.

NeuroVault​

NeuroVault is a repository for unthresholded statistical maps from neuroimaging studies.

As of early 2023, NeuroVault contains over 8,000 collections of statistical images, with over 100,000 images in total. It is the largest repository of unthresholded statistical maps in the world, and is the primary source of data for image-based meta-analyses using Neurosynth Compose.

Currently, NeuroVault supports some basic meta-analytic functionality. However, as other tools in this ecosystem are developed, -it is planned that NeuroVault will focus exclusively on image storage and sharing, and will rely on other tools for meta-analysis.

- +it is planned that NeuroVault will focus exclusively on image storage and sharing, and will rely on other tools for meta-analysis.

+ \ No newline at end of file diff --git a/introduction/faq.html b/introduction/faq.html index 6abc67d..c5dd26f 100644 --- a/introduction/faq.html +++ b/introduction/faq.html @@ -3,15 +3,15 @@ -Frequently Asked Questions | Neurosynth Compose Docs +Frequently Asked Questions | Neurosynth Compose Docs - +
-
- +

Frequently Asked Questions

  • How does this project relate to the original Neurosynth?

Neurosynth 1.0 was an online platform for browsing automatically generated large-scale neuroimaging meta-analyses. However, because all analyses were pre-generated, users were unable to define custom meta-analyses using the Neurosynth database. Instead, Neurosynth 1.0 used text mining techniques to automatically group studies based on the frequency of the terms mentioned in the text. Neurosynth Compose is focused on allowing users to overcome the limitations of automated large-scale meta-analysis, by enabling users to annotate studies, and curate sets of studies amenable for meta-analysis. This way, users can systematically define meta-analyses using their own expertise, while still leveraging the Neurosynth database, and an easy-to-use web-based analysis builder to accelerate the meta-analysis process.

You can read more about the relationship between Neurosynth 1.0 and Neurosynth Compose under Ecosystem

+ \ No newline at end of file diff --git a/introduction/team.html b/introduction/team.html index 8131869..7ba68c6 100644 --- a/introduction/team.html +++ b/introduction/team.html @@ -5,13 +5,13 @@ Our Team | Neurosynth Compose Docs - +
-

Our Team

Neurosynth-Compose is a collaborative effort between several labs around the world and is supported by the National Institute of Mental Health award 5R01MH096906-06.

Current Members​

  • Alejandro de la Vega

  • James Kent

  • Nicholas Lee

  • Taylor Salo

  • Katie Bottenhorn

  • JB Poline

  • Angela Laird

  • Russ Poldrack

  • Tom Nichols

  • Julio Pedraza

- +

Our Team

Neurosynth-Compose is a collaborative effort between several labs around the world and is supported by the National Institute of Mental Health award 5R01MH096906-06.

Current Members​

  • Alejandro de la Vega

  • James Kent

  • Nicholas Lee

  • Taylor Salo

  • Katie Bottenhorn

  • JB Poline

  • Angela Laird

  • Russ Poldrack

  • Tom Nichols

  • Julio Pedraza

+ \ No newline at end of file diff --git a/markdown-page.html b/markdown-page.html index 75606ea..8419d70 100644 --- a/markdown-page.html +++ b/markdown-page.html @@ -5,13 +5,13 @@ Markdown page example | Neurosynth Compose Docs - +

Markdown page example

You don't need React to write simple standalone pages.

- + \ No newline at end of file diff --git a/tutorial.html b/tutorial.html index 152e71f..cfa35e7 100644 --- a/tutorial.html +++ b/tutorial.html @@ -5,13 +5,13 @@ Tutorials | Neurosynth Compose Docs - +
-

Tutorials

Neurosynth-Compose supports a range of use cases, from a finely controlled manual-meta analysis to a fully automated large-scale meta-analysis.

Below is an overview of three uses cases, with links to tutorials for each one.

Automated

Fast exploratory analysis.

  • Query studies at scale
  • Search using terms, topics or activation coordinates
  • Replicate results from original Neurosynth
  • Immediate results, ideal for a exploratory analysis

Semi-Automated

Precise and customizable, but faster than manual.

  • Query NeuroStore to quickly find studies
  • Curate study inclusion to define concept more precisely
  • Optional fine-grained selection of analyses/contrasts within each study

Manual

Most stringent and rigorous.

  • Search across multiple sources, such as: PubMed, Web of Science, NeuroStore
  • Careful curation for inclusion/exclusion criteria
  • Extract coordinates from studies not already indexed
  • Meets PRISMA guidelines

- +

Tutorials

Neurosynth-Compose supports a range of use cases, from a finely controlled manual-meta analysis to a fully automated large-scale meta-analysis.

Below is an overview of three uses cases, with links to tutorials for each one.

Automated

Fast exploratory analysis.

  • Query studies at scale
  • Search using terms, topics or activation coordinates
  • Replicate results from original Neurosynth
  • Immediate results, ideal for a exploratory analysis

Semi-Automated

Precise and customizable, but faster than manual.

  • Query NeuroStore to quickly find studies
  • Curate study inclusion to define concept more precisely
  • Optional fine-grained selection of analyses/contrasts within each study

Manual

Most stringent and rigorous.

  • Search across multiple sources, such as: PubMed, Web of Science, NeuroStore
  • Careful curation for inclusion/exclusion criteria
  • Extract coordinates from studies not already indexed
  • Meets PRISMA guidelines

+ \ No newline at end of file diff --git a/tutorial/large-scale.html b/tutorial/large-scale.html index e5c2377..2e402d2 100644 --- a/tutorial/large-scale.html +++ b/tutorial/large-scale.html @@ -5,13 +5,13 @@ Exporatory automated large-scale meta-analysis | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/tutorial/manual.html b/tutorial/manual.html index 532d06f..c7fd6d3 100644 --- a/tutorial/manual.html +++ b/tutorial/manual.html @@ -5,13 +5,13 @@ Manual Meta-Analysis | Neurosynth Compose Docs - +
-
- + + \ No newline at end of file diff --git a/tutorial/semi-automated.html b/tutorial/semi-automated.html index e6add06..14b40cf 100644 --- a/tutorial/semi-automated.html +++ b/tutorial/semi-automated.html @@ -5,13 +5,13 @@ Semi-Automated Meta-Analysis with PRISMA | Neurosynth Compose Docs - +
-

Semi-Automated Meta-Analysis with PRISMA

- +

Semi-Automated Meta-Analysis with PRISMA

+ \ No newline at end of file