Manual
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Atlas & Assignment Tool 1 2 5 4 3 8 6 7 1) Coordinate panel Showing and changing the crosshair position 2) Figure settings Modifying the display of the orthogonal sections 3) Orthogonal sections Showing the MNI152 template in the background with the JuBrain Maximum Probability Map in lighter greyx 4). Overlay controls Load or remove an SPM map or an image overlay 5) JuBrain Voxel Assignment Cytoarchitectonic information for the crosshair location 6) JuBrain Cluster assignment Cytoarchitectonic information per overlay-cluster + Navigation through the overlay (SPM map, image) 8) Macroanatomical panel Assignment of the crosshair position and the current overlay cluster (if applicable) to the Harvard-Oxford macroanatomical atlas 7) Control panel Various controls including the change of font size (+ / - buttons) Coordinate panel Cross-hair position in MNI152 (world) space Cross-hair position in MPM voxel space Changing the coordinates (confirmed by ↩) moves the cross-hair and updates the voxel assignment Move cross-hair to origin Figure settings Toggle cross-hairs on / off (not affecting behavior) Zoom in/our focused on the cross-hair location Change the colormap of an overlay (not affecting the atlas & template display) Control panel Cycle through all clusters and save a screen-shot Screenshot Increase font size Save JuBrain assignment for all clusters as tsv Decrease font size Orthogonal sections In dark grey, the (non-linear) MNI152 template is shown, light grey represents the assignment to histological areas based on the JuBrain Maximum Probability Map. This map assigns each voxel to the most likely histological area at that position. Overlays, e.g., findings from functional or structural imaging studies may be overlayed on this map and are shown using the color-scale defined in the figure settings panel. Clicking on any of the three sections changes the cross-hair position to that location. In this process, the coordinate panel, the JuBrain voxel assignment and the macroanatomical information is updated. Overlay controls Bring up the SPM contrast manager, allowing you to define, evaluate and threshold contrasts Add an overlay image from a nifti-file. Premultiply: Multiply all image values by a scalar Hight threshold: Evaluated after pre-multiplication Extent threshold: In voxels (native image space) Remove the current overlay (only one overlay can be shown at any time) Overlays need to be in MNI152 space and are resampled to the template resolution (1 mm isotropic) JuBrain Voxel Assignment “Hard” assignment based on the Maximum Probability Map (MPM) Full description: probabilities for all histological area found at this position Information in this panel pertain (only) to the voxel at the cross-hair position Pointing the cursor on the name of a cytoarchitectonic area and keeping it there for ~1 second reveals the references describing the cytoarchitectonic mapping of this histological area. JuBrain Cluster assignment Use this menu to jump to the different clusters. Coordinates indicate the location of the cluster maximum This will update the JuBrain Voxel Assignment panel for information on maxima location Use this menu to jump to the different peaks (local maxima) within a cluster. Values in parenthesis indicate the overlay value (e.g., T / Z statistic). Comparison between the current cluster and the JuBrain MPM Overlap is provided relative to cluster and area (in brackets) volume (Eickhoff et al., 2005) Average probability for each JuBrain area at the location of the cluster relative to its full probability map Higher values indicate a location more towards the center of the area (cf. Eickhoff et al., 2007) Union of the probability values for each area at the location of the local maxima High values indicate that at least one peak was most likely located in the respective area give histological variability The Macroanatomical panel follows the same layout It is concurrently updated when a new cluster / maximum is selected
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File Type : PDF File Type Extension : pdf MIME Type : application/pdf Linearized : No Page Count : 5 PDF Version : 1.4 Title : Manual Producer : macOS Version 10.14.1 (Build 18B75) Quartz PDFContext Creator : PowerPoint Create Date : 2018:12:05 13:08:03Z Modify Date : 2018:12:05 13:08:03ZEXIF Metadata provided by EXIF.tools