info on atlas and autotrack usage

index.md

@@ -84,7 +84,7 @@ The thalamocortical structural connectivity tractography atlas was generated in
 >
 > In a container, this location is `/opt/dsi-studio/atlas/ICBM152_adult`. To use these files with a dsi-studio container, bind a local directory containing the contents of atlas/ICBM152_adult with these thalamus-specific .tt.gz and .tt.gz.txt files to the container directory (e.g., -B /cbica/projects/thalamocortical_development/software/thalamocortical_autotrack_template/dsi-studio/atlas/ICBM152_adult/:/opt/dsi-studio/atlas/ICBM152_adult). Or, bind the individual thalamus-specific .tt.gz and .tt.gz.txt files to their corresponding original files in /opt/dsi-studio/atlas/ICBM152_adult.
 >
->**It is highly recommended that you use this thalamocortical tractography atlas with the same autotrack parameters validated here for participant-specific data (see section "Delineation of Individual-Specific Thalamocortical Connections" below). These parameters include --otsu_threshold=0.5, --smoothing=1, --tolerance=10, --tip_iteration=0, --track_voxel_ratio=4, --check_ending=0, and (for command line usage) --yield_rate=0.0000001. Modifying the tolerance parameter may be reasonable to delineate even stricter trajectory-based pathways (lower the tolerance) or to allow for potential greater individual-specific differences in anatomy to emerge (increase the threshold). 
+>** It is highly recommended that you use this thalamocortical tractography atlas with the same autotrack parameters validated here for participant-specific data (see section "Delineation of Individual-Specific Thalamocortical Connections" below). These parameters include --otsu_threshold=0.5, --smoothing=1, --tolerance=10, --tip_iteration=0, --track_voxel_ratio=4, --check_ending=0, and (for command line usage) --yield_rate=0.0000001. Modifying the tolerance parameter may be reasonable to delineate even stricter trajectory-based pathways (lower the tolerance) or to allow for potential greater individual-specific differences in anatomy to emerge (increase the threshold). ** 
 
 ### Preprocessing and Reconstruction of Diffusion MRI Data (PNC and HCP-Development)
 Diffusion MRI data were preprocessed with qsiprep (0.14.2 for PNC; 0.16.1 for HCPD) as follows:
@@ -123,7 +123,7 @@ For HCPD, registration was accomplished with [/thalamocortical_structuralconnect
 --yield_rate=0.0000001  #yield rate that must be met before fiber tracking is terminated and no output is generated
 --export_template_trk=1  #write out reconstructed connection in dsi-studio template space
 ``` 
-*Note, thalamocortical_autotrack.sh was run twice (first to generate registration files, second to run autotrack on all atlas connections) due to how the threading parameter interacted with the registration process in dsi-studio. In recent versions of dsi-studio, greedy resource usage during registration was fixed, thus this procedure could now be run all in one step.
+Note, thalamocortical_autotrack.sh was run twice (first to generate registration files, second to run autotrack on all atlas connections) due to how the threading parameter interacted with the registration process in dsi-studio. In recent versions of dsi-studio, greedy resource usage during registration was fixed, thus this procedure could now be run all in one step.
 
 ### Quantification of Thalamocortical Connectivity Metrics
 Diffusion MRI-derived connectivity metrics (FA, MD, streamline count) and gene expression-derived thalamic gradient values (thalamus calbindin-parvalbumin CPt gradient) were extracted for every participant's autotrack-generated thalamocortical connections, using the following code: