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Testing the Dimensions with CIFTI Files

2026-01-13

Load MSC data and test data from cifti package

Using download_cifti_data() and download.file to download the test data.

library(cifti)
download_cifti_data(outdir = install_dir)

## [1] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/ones.dscalar.nii"                                     
## [2] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii" 
## [3] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.R.inflated.32k_fs_LR.surf.gii"                
## [4] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.L.inflated.32k_fs_LR.surf.gii"                
## [5] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69_AverageT1w_restore.nii.gz"                    
## [6] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii"
## [7] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii"    
## [8] "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpOoSPG4/filee204e8eb9b/cifti-2_test_data/Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii"

Here we will download a NIfTI file from the MSC dataset:

mscfile = file.path(
  install_dir, 
  "sub-MSC01_ses-func01_task-rest_bold_32k_fsLR.dtseries.nii")
if (!file.exists(mscfile)) {
  # url = paste0(
  #   "https://openneuro.org/crn/datasets/ds000224/snapshots/00002/files/", 
  #   "derivatives:", "surface_pipeline:", "sub-MSC01:",
  #   "processed_restingstate_timecourses:",  "ses-func01:cifti:",
  #   "sub-MSC01_ses-func01_task-rest_bold_32k_fsLR.dtseries.nii")
  url = paste0("https://s3.amazonaws.com/openneuro/ds000224/ds000224_R1.0.2/",
               "uncompressed/derivatives/surface_pipeline/sub-MSC01/", 
               "processed_restingstate_timecourses/ses-func01/cifti/", 
               "sub-MSC01_ses-func01_task-rest_bold_32k_fsLR.dtseries.nii")
  res = download.file(url = url, 
    destfile = mscfile, mode = "wb")
  stopifnot(file.exists(mscfile))
}

test_dir = file.path(install_dir, "cifti-2_test_data")

ds <- read_cifti(
  file.path(test_dir,
            "Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii")
  )

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

dt <- read_cifti(
  file.path(test_dir,
            "Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii")
  )

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

pt <- read_cifti(
  file.path(test_dir,
            "Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii")
  )

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

dl <- read_cifti(
  file.path(test_dir, 
            "Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii") 
  )

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

msc <- read_cifti(mscfile, trans_data = FALSE)

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

msc_trans <- read_cifti(mscfile, trans_data = TRUE)

## Parsing Volume Data

## Parsing Surface Data

## Parsing Parcel Data

## Parsing Named Map Data

## Parsing Brain Model Data

For reference: MSC 01 (65890 * 818) (using matlab ft_read_cifti), showing first 5 rows & columns

##            V1       V2       V3       V4       V5
## [1,]  1.60060  2.27580  1.60540  0.12593 -0.49364
## [2,]  1.85790  2.55780  1.59500 -0.84614 -2.63840
## [3,]  0.33651  1.46200  1.77790  0.34857 -1.93580
## [4,]  0.95052  0.71743 -0.94483 -2.33310 -2.10040
## [5,] -2.08590 -1.99750 -1.24970 -0.93712 -0.58043

MSC Sub-01 Session 1 (sub-MSC01_ses-func01_task-rest_bold_32k_fsLR.dtseries.nii)

read_cifti(fname = , trans_data = FALSE) * header dimension shows 65890 * 818 * read in file shows 65890 * 818 by setting trans_data to FALSE

msc$hdr

## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 3002 ()
##   Qform Code      : 0 (Unknown)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 1 x 1 x 1 x 1 x 65890 x 818
##   Pixel Dimension : 1 x 1 x 1 x 1 x 1 x 1
##   Voxel Units     :
##   Time Units      : sec

dim(msc$data)

## [1] 65890   818

msc$data[1:5,1:5]

##           [,1]      [,2]      [,3]      [,4]      [,5]
## [1,]  1.600599  2.275847  1.605402  0.125929 -0.493640
## [2,]  1.857941  2.557801  1.595005 -0.846137 -2.638434
## [3,]  0.336508  1.461959  1.777888  0.348566 -1.935833
## [4,]  0.950522  0.717431 -0.944832 -2.333094 -2.100426
## [5,] -2.085948 -1.997536 -1.249652 -0.937115 -0.580428

If transpose is not set to FALSE (default is TRUE), it will return a 818 * 65890 that is filled correctly, and user just have to t() the cii$data

t(msc_trans$data[1:5,1:5])

##           [,1]      [,2]      [,3]      [,4]      [,5]
## [1,]  1.600599  2.275847  1.605402  0.125929 -0.493640
## [2,]  1.857941  2.557801  1.595005 -0.846137 -2.638434
## [3,]  0.336508  1.461959  1.777888  0.348566 -1.935833
## [4,]  0.950522  0.717431 -0.944832 -2.333094 -2.100426
## [5,] -2.085948 -1.997536 -1.249652 -0.937115 -0.580428

Data where dimensions are row x dense loads fine. Updated function loads them the same way as before.

Conte69.MyelinAndCorrThickness.32k_fs_LR.dscalar.nii

Dense file “d”, vertex level data
Header shows dimension as rows * dense

ds$hdr

## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 3006 ()
##   Qform Code      : 0 (Unknown)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 1 x 1 x 1 x 1 x 2 x 60951
##   Pixel Dimension : 1 x 1 x 1 x 1 x 1 x 1
##   Voxel Units     :
##   Time Units      : sec

attributes(ds$BrainModel[[1]])

## $IndexOffset
## [1] 0
## 
## $IndexCount
## [1] 30424
## 
## $BrainStructure
## [1] "CIFTI_STRUCTURE_CORTEX_LEFT"
## 
## $ModelType
## [1] "CIFTI_MODEL_TYPE_SURFACE"
## 
## $SurfaceNumberOfVertices
## [1] 32492

attributes(ds$BrainModel[[2]])

## $IndexOffset
## [1] 30424
## 
## $IndexCount
## [1] 30527
## 
## $BrainStructure
## [1] "CIFTI_STRUCTURE_CORTEX_RIGHT"
## 
## $ModelType
## [1] "CIFTI_MODEL_TYPE_SURFACE"
## 
## $SurfaceNumberOfVertices
## [1] 32492

dim(ds$data)

## [1] 60951     2

head(ds$data)

##          [,1]     [,2]
## [1,] 1.321855 3.195882
## [2,] 1.373803 2.141433
## [3,] 1.408264 3.028383
## [4,] 1.244012 3.237031
## [5,] 1.479665 2.216135
## [6,] 1.266741 2.795304

Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii

dt$hdr

## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 3002 ()
##   Qform Code      : 0 (Unknown)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 1 x 1 x 1 x 1 x 2 x 60951
##   Pixel Dimension : 1 x 1 x 1 x 1 x 1 x 1
##   Voxel Units     :
##   Time Units      : sec

attributes(dt$BrainModel[[1]])

## $IndexOffset
## [1] 0
## 
## $IndexCount
## [1] 30424
## 
## $BrainStructure
## [1] "CIFTI_STRUCTURE_CORTEX_LEFT"
## 
## $ModelType
## [1] "CIFTI_MODEL_TYPE_SURFACE"
## 
## $SurfaceNumberOfVertices
## [1] 32492

attributes(dt$BrainModel[[2]])

## $IndexOffset
## [1] 30424
## 
## $IndexCount
## [1] 30527
## 
## $BrainStructure
## [1] "CIFTI_STRUCTURE_CORTEX_RIGHT"
## 
## $ModelType
## [1] "CIFTI_MODEL_TYPE_SURFACE"
## 
## $SurfaceNumberOfVertices
## [1] 32492

dim(dt$data)

## [1] 60951     2

head(dt$data)

##          [,1]     [,2]
## [1,] 1.321855 3.195882
## [2,] 1.373803 2.141433
## [3,] 1.408264 3.028383
## [4,] 1.244012 3.237031
## [5,] 1.479665 2.216135
## [6,] 1.266741 2.795304

Conte69.MyelinAndCorrThickness.32k_fs_LR.ptseries.nii

parcel level

pt$hdr

## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 3004 ()
##   Qform Code      : 0 (Unknown)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 1 x 1 x 1 x 1 x 2 x 54
##   Pixel Dimension : 1 x 1 x 1 x 1 x 1 x 1
##   Voxel Units     :
##   Time Units      : sec

dim(pt$data)

## [1] 54  2

head(pt$data)

##          [,1]     [,2]
## [1,] 1.431012 2.515503
## [2,] 1.392534 2.339441
## [3,] 1.521327 2.154038
## [4,] 1.498012 1.684434
## [5,] 1.618780 2.652969
## [6,] 1.511189 2.089453

Conte69.parcellations_VGD11b.32k_fs_LR.dlabel.nii (dense label on vertex level)

dense label

dl$hdr

## NIfTI-1 format
##   Type            : nifti
##   Data Type       : 16 (FLOAT32)
##   Bits per Pixel  : 32
##   Slice Code      : 0 (Unknown)
##   Intent Code     : 3007 ()
##   Qform Code      : 0 (Unknown)
##   Sform Code      : 0 (Unknown)
##   Dimension       : 1 x 1 x 1 x 1 x 3 x 64984
##   Pixel Dimension : 1 x 1 x 1 x 1 x 1 x 1
##   Voxel Units     :
##   Time Units      : sec

dim(dl$data)

## [1] 64984     3

head(dl$data)

##      [,1] [,2] [,3]
## [1,]    0   67    0
## [2,]    0   59    0
## [3,]    8   56    0
## [4,]    8   54    0
## [5,]   14   87    0
## [6,]    0   64    0

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.