questions > about dicom with multiple slice
Showing 1-6 of 6 posts
Dec 4, 2020 08:12 AM | Sidi Ma
about dicom with multiple slice
I have some dicom files about hearts. It has 50 time frames and 10
slices for a individual's heart.
So the data matrix shape is 208(row number)*186(columns number)*6(slice number)*50(time frame number).
Here I want to transform this matrix to a nifti format. I can transform every slice to a nifti format with using dcm2nii.
But how to transform these 10 slices to a nifti file all together. My procedure need a 208*186*6*50 matrix to label cavities. Which parameter should I use to do complete this object?
So the data matrix shape is 208(row number)*186(columns number)*6(slice number)*50(time frame number).
Here I want to transform this matrix to a nifti format. I can transform every slice to a nifti format with using dcm2nii.
But how to transform these 10 slices to a nifti file all together. My procedure need a 208*186*6*50 matrix to label cavities. Which parameter should I use to do complete this object?
Dec 4, 2020 03:12 PM | Chris Rorden
RE: about dicom with multiple slice
what happens if you run the command 'dcm2niix -f %s_%p_%t
/path/to/DICOM'? All dcm2niix does is stack series as defined by
the DICOM images. If your data is all part of the same series, all
the slices should be combined into a single file. If your data is
acquired as different series, you could merge your NIfTI images
with fslmerge. The output provided by dcm2niix typically provides
insights into the properties that caused images to be stacked or
separated (e.g. for MRI data echo time, coil used, slice
orientation, etc. can all be reasons slices from the same series
are not merged). Sometimes using the parameter "-m y" or "-m n" may
change how slices are combined, but this is usually a Hail Mary for
poorly specified DICOM data.
Dec 11, 2020 04:12 AM | Sidi Ma
RE: about dicom with multiple slice
Sorry for the delay....
It looks like my dataset are comprise of different series. This is file structure showed by MicroDicom viewer:
All patients(Ptients:1, Images: 1453)
XXXXXXXX
YYYY heart(MR: 15 series)
CINE segmented_SAX_b1
CINE segmented_SAX_b2
CINE segmented_SAX_b3
CINE segmented_SAX_b4
CINE segmented_SAX_b5
CINE segmented_SAX_b6
CINE segmented_SAX_b7
CINE segmented_SAX_b8
CINE segmented_SAX_b9
CINE segmented_SAX_b10
CINE segmented_SAX_b11
CINE segmented_SAX_b12
CINE segmented_SAX_b13
CINE segmented_SAX_InlineVF
Inline_VF_Results
This is a heart short axis MRI data.
The different series mean different location heart slices with each slice having 50 time frames.
should I merge my NIfTI images transformed by dcm2nii with fslmerge?
It looks like my dataset are comprise of different series. This is file structure showed by MicroDicom viewer:
All patients(Ptients:1, Images: 1453)
XXXXXXXX
YYYY heart(MR: 15 series)
CINE segmented_SAX_b1
CINE segmented_SAX_b2
CINE segmented_SAX_b3
CINE segmented_SAX_b4
CINE segmented_SAX_b5
CINE segmented_SAX_b6
CINE segmented_SAX_b7
CINE segmented_SAX_b8
CINE segmented_SAX_b9
CINE segmented_SAX_b10
CINE segmented_SAX_b11
CINE segmented_SAX_b12
CINE segmented_SAX_b13
CINE segmented_SAX_InlineVF
Inline_VF_Results
This is a heart short axis MRI data.
The different series mean different location heart slices with each slice having 50 time frames.
should I merge my NIfTI images transformed by dcm2nii with fslmerge?
Dec 11, 2020 11:12 AM | Chris Rorden
RE: about dicom with multiple slice
Your data are explicitly stored in different series. Therefore, the
DICOM images are explicitly instructing dcm2niix to store these as
separate images. You could use fslmerge or a simple Matlab script to combine series.
Dec 18, 2020 10:12 AM | Sidi Ma
RE: about dicom with multiple slice
I have searched the fslmerge and found a R
function https://rdrr.io/cran/fslr/man/fslmerge.html and a python
function https://pythonhosted.org/nipype/interfaces/generated/nipype.interfaces.fsl.utils.html . Are these function
equal?
It looks like all functions do are concatenating these matrix to a new matrix with a additional dimension. Is this right?
It looks like all functions do are concatenating these matrix to a new matrix with a additional dimension. Is this right?