finalsample_PNC.Rmd

---
title: "PNC Final Sample Selection: Thalamocortical Development"
author: "Valerie Jill Sydnor"
output:
  html_document:
    code_folding: show
    highlight: haddock
    theme: lumen
    toc: yes
    toc_depth: 4
    toc_float: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
require(dplyr)
```

# Initial Participant List

```{r}
#list of RBC ids with processed, non-variant diffusion MRI data, N = 1358
participants <- read.csv("/cbica/projects/thalamocortical_development/sample_info/PNC/PNC_NonVariantDWI_participantlist.txt", header=F)
colnames(participants) <- c("rbcid") 
```

# Match rbcid, bblid, and scanid

```{r}
id.key <- read.csv("/cbica/projects/thalamocortical_development/sample_info/PNC/bblid_scanid_reid.csv") #bblid-scanid-rbcid match
id.key$rbcid <- paste0("sub-", id.key$rbcid)
participants <- left_join(participants, id.key, by="rbcid") 
```

# Construct Final Sample

Health Exclusion

```{r}
healthexclude <- read.csv("/cbica/projects/thalamocortical_development/sample_info/PNC/n1601_health_20170421.csv")
healthinclude <- healthexclude %>% filter(healthExcludev2 == 0) %>% dplyr::select(scanid) 

participants.final <- participants[participants$scanid %in% healthinclude$scanid,] #remove 118 health exclude participants from the initial sample of 1358 with non-variant diffusion data, remaining N = 1240
```

T1 Quality Exclusion

```{r}
T1exclude <- read.csv("/cbica/projects/thalamocortical_development/sample_info/PNC/n1601_t1QaData_20170306.csv")
T1include <- T1exclude %>% filter(t1Exclude == 0) %>% dplyr::select(scanid)

participants.final <- participants.final[participants.final$scanid %in% T1include$scanid,] #remove 25 participants with bad T1 data, remaining N = 1215
```

Diffusion Quality Exclusion

```{r}
dwi.qc <- read.csv("/cbica/projects/thalamocortical_development/sample_info/PNC/PNC_DWI_QCmetrics.csv") #diffusion scan acquisition parameters and quality metrics, generated by sample_construction/PNC/diffusion_qcmetrics_PNC.py

qualityexclude <- dwi.qc %>% filter(t1_neighbor_corr < 0.9) %>% select(subject_id) #participants to exclude from the final study sample based on processed diffusion MRI T1 neighborhood correlation

participants.final <- participants.final[!participants.final$rbcid %in% qualityexclude$subject_id,]  #remove 57 participants from the sample of 1215 due to diffusion data quality, remaining N = 1158
```

Diffusion Scan Head Motion Exclusion

```{r}
motionexclude <- dwi.qc %>% filter(mean_fd > 1) %>% select(subject_id) #participants to exclude from the final study sample based on high in-scanner head motion during the diffusion runs #kids are wiggly

participants.final <- participants.final[!participants.final$rbcid %in% motionexclude$subject_id,] #remove 13 participants from the sample of 1158 due to in-scanner head motion, remaining N = 1145
```

# Save Final Sample

```{r}
write.csv(participants.final, "/cbica/projects/thalamocortical_development/sample_info/PNC/PNC_thalamocortical_finalsample_N1145.csv", quote = F, row.names = F)
```