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--- jvs:fscan:here [2011/08/29 16:50]
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+++ jvs:fscan:here [2011/09/01 18:10]
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-==== fScan versus other fMRI analysis software ====
+==== How fScan differs from other fMRI programs ====
-fScan differs from other fMRI analysis software in 3 important ways: 1) organization of
+fScan differs from other fMRI analysis software in 3 important ways: 1) organization of multimodal data in coherent XML-based “workspace” descriptor files and the ability to compare
-multimodal data in coherent XML-based “workspace” descriptor files and the ability to compare
+two workspaces simltaneously, 2) integration and interoperability of fScan’s large repertoire of intrinsic processing features with the ability to run programs and read data from other software packages all within a single fScan interactive session, 3) emphasis on data visualization capabilities, multimodal data integration, and a comprehensive and user-friendly graphical user interface.
-two workspaces simltaneously, 2) integration and interoperability of fScan’s large repertoire of
-intrinsic processing features with the ability to run programs and read data from other software
+) **Workspaces** – A workspace is a collection of any number of related data_sets. Within a workspace, all spatial data can be registered to a common spatial coordinate system so that
-packages all within a single fScan interactive session, 3) emphasis on data visualization
+any location in one data set can be directly mapped onto any other data set. Examples of spatial data can be a single 2-dimensional JPEG image, or a large 3-D, 4-D (or even 5-D or
-capabilities, multimodal data integration, and a comprehensive and user-friendly graphical user
+-D) series of MR images, or a 3D surface reconstruction graphics data set. A workspace also binds multiple time series data sets to a common temporal coordinate system. For
-interface. The relevance of each of these for the proposed study is briefly discussed.
+example, it can link stimulus and behavioral response timing files, physiological oscillation data, eye-tracking data, and fMRI functional imaging data so that the relative timing is
-) Workspaces – A workspace is a collection of any number of related data_sets. Within a
+accurately known across all data collected for each brain scan. All information describing a workspace can be saved in a single XML text file. fScan can load two different workspaces
-workspace, all spatial data can be registered to a common spatial coordinate system so that
+simultaneously and the spatial coordinate systems of both can be registered, which then allows any data set in one workspace to be overlaid or compared to spatial data in the other.
-any location in one data set can be directly mapped onto any other data set. Examples of
+Originally designed to facilitate comparison between a subject exam workspace and a standard brain atlas workspace, this ability can also prove invaluable for comparing and quantifying changes in brain function (or structure) across multiple scan sessions of a single subject.
-spatial data can be a single 2-dimensional JPEG image, or a large 3-D, 4-D (or even 5-D or
--D) series of MR images, or a 3D surface reconstruction graphics data set. A workspace
+) **Interoperability** – fScan's processing capabilities are not limited to its own internally programmed features. It also supports in-line execution of other software packages. For
-also binds multiple time series data sets to a common temporal coordinate system. For
+example, to use FSL's motion correction program (MCFLIRT) a user simply clicks an icon in the "FSL" taskbar to start a a shell script that automatically reformats the appropriate data file
-example, it can link stimulus and behavioral response timing files, physiological oscillation
+to NIfTI format if necessary, runs the MCFLIRT program, and then returns to the waiting fScan process to automatically load the newly created data set into a new fScan window. New data sets produced in that way are automatically registered to the common workspace coordinate system. This shell scripting option provides enormous flexibility to combine fScan's own internal features with complementary features available in other software packages. Simple graphical taskbars currently provide access to most major FSL package features and provide full integration of FreeSurfer 3-D brain reconstruction data. Additional interoperability taskbars are being added to integrate AFNI (Cox et al., 1996) software programs as well as DTI programs and data structures.
-data, eye-tracking data, and fMRI functional imaging data so that the relative timing is
-accurately known across all data collected for each brain scan. All information describing a
+) **Visualization environment** – fScan’s taskbar GUI interface is designed to be intuitively easy to use, and fScan's help features are simple and always available via direct access to a web-
-workspace can be saved in a single XML text file. fScan can load two different workspaces
+based Wiki that can be easily kept up-to-date. By providing immediate access to all data components via a common workspace, a simple graphical interface to processing features in
-simultaneously and the spatial coordinate systems of both can be registered, which then
+fScan and multiple other programs, and extensive data visualization tools fScan can make functional brain mapping very accessible even to non-expert users. The result is a
-allows any data set in one workspace to be overlaid or compared to spatial data in the other.
+powerful brain image analysis platform that will provide the foundation for thorough image data analyses. It cab also be used as a valuable teaching tool for providing students and others
-Originally designed to facilitate comparison between a subject exam workspace and a
+with direct access to collected data and to brain mapping methods more generally.
-standard brain atlas workspace, this ability to compare two sessions will be invaluable in the
-proposed longitudinal study for comparing and quantifying changes in brain function (or
-structure) across multiple scan sessions of a single subject.
-) Interoperability – fScan's processing capabilities are not limited to its own internally
-programmed features. It also supports in-line execution of other software packages. For
-example, to use FSL's motion correction program (MCFLIRT) a user simply clicks an icon in
-the "FSL" taskbar to start a a shell script that automatically reformats the appropriate data file
-to NIfTI format if necessary, runs the MCFLIRT program, and then returns to the waiting
-fScan process to automatically load the newly created data set into a new fScan window.
-New data sets produced in that way are automatically registered to the common workspace
-coordinate system. This shell scripting option provides enormous flexibility to combine
-fScan's own internal features with complementary features available in other software
-packages. Simple graphical taskbars currently provide access to most major FSL package
-features and provide full integration of FreeSurfer 3-D brain reconstruction data. Additional
-interoperability taskbars are being added to integrate AFNI (Cox et al., 1996) software
-programs as well as DTI programs and data structures.
-) Visualization environment – fScan’s taskbar GUI interface is designed to be intuitively easy to
-use, and fScan's help features are simple and always available via direct access to a web-
-based Wiki that can be easily kept up-to-date. By providing immediate access to all data
-components via a common workspace, a simple graphical interface to processing features in
-fScan and multiple other programs, and extensive data visualization tools fScan can make
-functional brain mapping very accessible even to non-expert users. As part of our preliminary
-studies and preparation for the current proposal we have been directly involved in improving
-fScan’s user interface, user tutorials, and other on-line documentation. The result is a
-powerful brain image analysis platform that will provide the foundation for our image data
-analyses. It will also be used as a valuable teaching tool for providing students and others
-with direct access to the data collected in this study and to brain mapping methods more
-generally.

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