scripts used for analysis of PINT in SZ samples
It docker is installed. Start the rstudio env. Set your current directory to base of this repo
docker-compose up rstudioMy change here.
This is a repo of code (and some data links), relating to the manuscript in preparation:
.
├── code
│ ├── bin
│ │ └── subcortical_extraction_20171121.sh
│ └── R
│ └── ...settings_helpers.R
├── data
│ ├── processed
│ │ ├── mri
│ │ ├── pheno
│ │ └── Rdata_cache
│ └── raw
│ ├── bids
│ ├── phenotypic
│ ├── restricted_pheno
│ └── templates
│ ├── ...
│ ├── Yeo7_2011_80verts.csv
│ ├── Yeo7_2011_80verts_roiidx_LUT.txt
│ └── Yeo7_2011_80vertx_coords.labels
├── LICENSE
├── notebooks
│ ├── preproc_md
│ │ └── ..
│ └── Rmd
│ ├── 01a_mangle_participant_dems.Rmd
│ ├── 01b_mangle_scanQA_covars.Rmd
│ ├── 02a_pint_displacement_stats.Rmd
│ ├── 02b_MDS_stats.Rmd
│ ├── 02c_seedcorr_area_stats.Rmd
│ ├── 03_subcortical_cortical_stats_hemi.Rmd
│ ├── 04_cortical-cortical_changes.Rmd
│ ├── 05_sulcal_depth_stats.Rmd
│ ├── 06_whole_matrix_stats.Rmd
│ ├── _bookdown.yml
│ ├── index.Rmd
│ ├── _output.yml
│ ├── preamble.tex
│ └── zz_otherstuff
├── README.md
├── reports
│ ├── other_figures
│ │ └── vertex_probmaps
│ └── Rmd_rendered
├── SZ_PINT.Rproj
└── zz_deprecated
Note: in my local (tigrlab version) of this subfolders in this repo are symlinks to locations on the tigrlab servers..
├── data
│ ├── processed
│ │ ├── mri -> ../../../../../../scratch/edickie/saba_PINT/ciftify_fmriprep/
├── data
│ └── raw
│ ├── bids
│ │ └── ds000030 -> ../../../../../../../scratch/edickie/saba_PINT/bids_in/ds000030/ds000030_R1.0.5/
├── data
│ └── raw
│ ├── restricted_phenoicalData
│ │ ├── COBRE -> ../../../../../external/SchizConnect/COBRE
│ │ └── ZHH -> ../../../../../../../external/ZHH_rest/