revision

index.md

@@ -193,6 +193,7 @@ Three sensitivity analyses were conducted to ensure that developmental findings
 * For the surface area analyses, T1w images were analyzed with FreeSurfer 6.0.1. [freesurfer_tabulate](https://github.com/PennLINC/freesurfer_tabulate) was then applied to processed anatomical data to calculate the surface area of regions included in the HCP-MMP atlas.
 * For the tSNR analysis, the voxel-wise map of b=0 shell tSNR was obtained from FSL eddy outputs generated during QSIPrep. The average tSNR was then computed in masks of all participants' thalamocortical connections by running [/tract_measures/snr/thalamocortical_SNR_jobs.sh](https://github.com/PennLINC/thalamocortical_development/blob/main/tract_measures/snr/thalamocortical_SNR_jobs.sh), which launches [/tract_measures/snr/thalamocortical_calculate_SNR.sh](https://github.com/PennLINC/thalamocortical_development/blob/main/tract_measures/snr/thalamocortical_calculate_SNR.sh) for each participant. SNR data were collated into dataset-specific csvs using [/tract_measures/snr/thalamocortical_SNRvalues.py](https://github.com/PennLINC/thalamocortical_development/blob/main/tract_measures/snr/thalamocortical_SNRvalues.py).
 * For the atlas overlap analysis, sensitivity (true positive rates) were used.
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 To create dataframes with connection-specific sensitivity variables while excluding connections with < 5 streamlines from analysis, [/sample_construction/PNC/tractmeasures_sensitivity_PNC.R](https://github.com/PennLINC/thalamocortical_development/blob/main/sample_construction/PNC/tractmeasures_sensitivity_PNC.R) was run along with [/sample_construction/HCPD/tractmeasures_sensitivity_HCPD.R](https://github.com/PennLINC/thalamocortical_development/blob/main/sample_construction/HCPD/tractmeasures_sensitivity_HCPD.R). Sensitivity development GAMs were then fit using these dataframes in [/gam_functions/fit_sensitivityGams.R](https://github.com/PennLINC/thalamocortical_development/blob/main/gam_functions/fit_sensitivityGams.R). Finally, the results of sensitivity analyses are presented in [/results/sensitivity_analyses/thalamocortical_development_sensitivity.Rmd](https://github.com/PennLINC/thalamocortical_development/blob/main/results/sensitivity_analyses/thalamocortical_development_sensitivity.Rmd) which can be viewed [here](https://htmlpreview.github.io/?https://github.com/PennLINC/thalamocortical_development/blob/main/results/sensitivity_analyses/thalamocortical_development_sensitivity.html).  
 
 # DIFFUSION DATA AVAILABILITY