Nothing
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- eval = FALSE-------------------------------------------------------
# # install.packages("devtools")
# devtools::install_github("adigherman/nitrcbot")
## ---- eval = FALSE-------------------------------------------------------
# set_credentials(username = "XXX", password = "YYY")
## ---- eval = FALSE-------------------------------------------------------
# nitrc_sets <- nitrcbot::list_image_sets()
# nitrc_sets_summary <- nitrc_sets[,c("ID","Name","Subjects")]
## ---- eval = FALSE-------------------------------------------------------
# nitrc_sets_summary
# ID Name Subjects
# 1 kin Kurtosis Imaging Network 81
# 2 studyforrest_rev003 Study Forrest rev003 20
# 3 nki_rockland INDI NKI/Rockland Sample 207
# 4 PING Pediatric Imaging, Neurocognition, and Genetics (PING) Study 0
# 5 ixi IXI dataset 584
# 6 parktdi High-quality diffusion-weighted imaging of Parkinson's disease 53
# 7 cs_schizbull08 CANDI Share: Schizophrenia Bulletin 2008 103
# 8 short_tr Beijing Short TR 28
# 9 beijing_eoec Beijing Eyes Open Eyes Closed 48
# 10 beijing_enh Beijing Enhanced 180
# 11 ABIDE ABIDE 1112
# 12 corr Consortium for Reliability and Reproducibility (CoRR) 1386
# 13 fcon_1000 1000 Functional Connectomes 1288
# 14 adhd_200 ADHD-200 973
## ---- eval = FALSE-------------------------------------------------------
# ixi_project <- read_nitrc_project('ixi')
# head(ixi_project)
# ID label project gender handedness session_ID scan_ID age
# 1 NITRC_IR_S05189 2 ixi female NITRC_IR_E10452 PD 35.8
# 2 NITRC_IR_S05189 2 ixi female NITRC_IR_E10452 T1 35.8
# 3 NITRC_IR_S05189 2 ixi female NITRC_IR_E10452 MRA 35.8
# 4 NITRC_IR_S05189 2 ixi female NITRC_IR_E10452 DTI 35.8
# 5 NITRC_IR_S05189 2 ixi female NITRC_IR_E10452 T2 35.8
# 6 NITRC_IR_S05190 12 ixi male NITRC_IR_E10453 T1 38.78
## ---- eval = FALSE-------------------------------------------------------
# ixi_T1_males = ixi_project %>%
# filter(gender %in% "male") %>%
# filter(scan_ID %in% "T1") %>%
# select(ID, session_ID) %>%
# unique
# head(ixi_T1_males)
## ---- eval = FALSE-------------------------------------------------------
# ID session_ID
# 1 NITRC_IR_S05190 NITRC_IR_E10453
# 2 NITRC_IR_S05191 NITRC_IR_E10454
# 3 NITRC_IR_S05193 NITRC_IR_E10456
# 4 NITRC_IR_S05194 NITRC_IR_E10457
# 5 NITRC_IR_S05196 NITRC_IR_E10459
# 6 NITRC_IR_S05197 NITRC_IR_E10460
## ---- eval = FALSE-------------------------------------------------------
# t1_res <- download_nitrc_dir("NITRC_IR_E10453", scan_type="T1")
# t1_res$files
# [1] "77390_IXI012-HH-1211-T1.nii.gz" "77391_qc_t.gif" "77391_qc.gif"
## ---- eval = FALSE-------------------------------------------------------
# > download_nitrc_dir("NITRC_IR_E10453", scan_type="T1", zipped = TRUE)
# [1] "/var/folders/kr/05bm5krj0r3fpwxfdmx4xthm0000gn/T//RtmpVWPpmG/NITRC_IR_E10453.zip"
## ---- eval = FALSE-------------------------------------------------------
# r <- get_scan_resources('NITRC_IR_E10453')
# > head(r$URI)
# [1] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-00.nii.gz"
# [2] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-01.nii.gz"
# [3] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-02.nii.gz"
# [4] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-03.nii.gz"
# [5] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-04.nii.gz"
# [6] "/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-05.nii.gz"
## ---- eval = FALSE-------------------------------------------------------
# > download_nitrc_file("/data/experiments/NITRC_IR_E10453/scans/DTI/resources/77382/files/IXI012-HH-1211-DTI-05.nii.gz")
# [1] "/var/folders/kr/05bm5krj0r3fpwxfdmx4xthm0000gn/T//RtmpVWPpmG/IXI012-HH-1211-DTI-05.nii.gz"
## ---- eval = FALSE-------------------------------------------------------
# > get_scan_params('NITRC_IR_E11033')
# type imagescandata_id TR TE flip matrix_X matrix_Y voxel_X voxel_Y voxel_Z frames partitions fieldStrength quality
# 1 DTI 44882 9054.01 80.0 90
# 2 MRA 44883 20.0 6.9052 25
# 3 PD 44884 8178.34 8.0 90
# 4 T1 44885 9.813 4.603 8
# 5 T2 44886 8178.34 100.0 90
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