converting 3D nii files to 4D

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1

Dear 3D slicer community,
I have 50 3D nii files that I want to convert them to 4D nii and view it as a movie.I wonder if 3D slicer has this ability.
Thanks,

2

You can view 4D volumes as movies (for example, using Volume Rendering) in Slicer. You can also export it as a mp4 video (using Screen Capture module), register, segment, analyze, etc.

4D volume sequences can be saved as nrrd files in Slicer. If you must save as nifti then you should be able to find Python packages that can import a 4D nrrd image and save it as 4D nifti.

3

@lassoan I have combined 3 scalar 3D volumes (Flair, T1, TRACE) into and saved it as NRRD format.

1: When I have done this, as a “3D vector image” it always looks like it is displayed as an RGB image

2: When I concatenate into a 4D data set, the nrrd file only loads 1 scalar value, and it looses it’s physical space representation.

I was expecting something akin to the DWI dataset to be loaded with an index for each component.

import itk

ADCfn = "ADCSkullStrippedregistered.nii.gz"
FLfn = "FLAIRSkullStrippedregistered.nii.gz"
TRfn = "TRACEWSkullStrippedregistered.nii.gz"

DTYPE = itk.F
SIZE = 3
IMTYPE = itk.Image[DTYPE, SIZE]
VIMTYPE = itk.VectorImage[DTYPE, SIZE]
D4IMTYPE= itk.Image[DTYPE, 4]

jif = itk.JoinSeriesImageFilter[IMTYPE,D4IMTYPE].New()

ADC = itk.imread(ADCfn, pixel_type=DTYPE)
FL = itk.imread(FLfn, pixel_type=DTYPE)
TR = itk.imread(TRfn, pixel_type=DTYPE)

resample_ADC2FL = itk.ResampleImageFilter[IMTYPE,IMTYPE].New()
resample_ADC2FL.SetInput(ADC)
resample_ADC2FL.SetReferenceImage(FL)
resample_ADC2FL.UseReferenceImageOn()
resample_ADC2FL.Update()
rADC=resample_ADC2FL.GetOutput()

resample_TR2FL  = itk.ResampleImageFilter[IMTYPE,IMTYPE].New()
resample_TR2FL.SetInput(TR)
resample_TR2FL.SetReferenceImage(FL)
resample_TR2FL.UseReferenceImageOn()
resample_TR2FL.Update()
rTR=resample_TR2FL.GetOutput()

cif = itk.ComposeImageFilter[IMTYPE, VIMTYPE].New()
cif.SetInput(0, rTR)
cif.SetInput(1, rADC)
cif.SetInput(2, FL)
cif.SetInput(3, FL)
cif.SetInput(4, FL)
cif.Update()

output = cif.GetOutput()
itk.imwrite(output,"/tmp/test.nrrd")

jif = itk.JoinSeriesImageFilter[IMTYPE,D4IMTYPE].New()
jif.SetInput(0, rTR)
jif.SetInput(1, rADC)
jif.SetInput(2, FL)
jif.SetInput(3, FL)
jif.SetInput(4, FL)
jif.Update()

output = jif.GetOutput()
itk.imwrite(output,"/tmp/test4d.nrrd")

nrrd header for the 3D vector image

NRRD0004 
# Complete NRRD file format specification at: 
# http://teem.sourceforge.net/nrrd/format.html 
type: float 
dimension: 4 
space: left-posterior-superior 
sizes: 5 320 320 20 
space directions: none (0.74917204642169,0.013089305043978788,-0.032709554472705113) (0.013076845101263054,-0.74988577139539259,-0.000570947400907372) (0.3053356701418492,-4.0745362190901257e-10,6.9933375528812443) 
kinds: vector domain domain domain 
endian: little
encoding: raw
space origin: (-108.57624816894531,90.696868896484375,-87.553054809570312)

nrrd header for the concatenated 4D scalar volumes

NRRD0004
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: float
dimension: 4
space dimension: 4
sizes: 320 320 20 5
space directions: (0.74917204642169,0.013089305043978788,-0.032709554472705113,0) (0.013076845101263054,-0.74988577139539259,-0.000570947400907372,0) (0.3053356701418492,-4.0745362190901257e-10,6.9933375528812443,0) (0,0,0,1)
kinds: domain domain domain domain
endian: little
encoding: raw
space origin: (-108.57624816894531,90.696868896484375,-87.553054809570312,0)