Similalry, something is very wrong with the spatial information, since if I try to convert the dicom to the nifti format with dcm2niix, the directions are reversed: superior is down and inferior is up, forward is back and backward is front. What step am I missing ? python-3.x...
I'm trying to convert a slew of DTI siemens DICOMs to NifTi using freesurfer's dcm2nii utility but am failing on some files because they are missing the DiffusionGradientDirection tag (0x19,0x100E), which is necessary to generate the .bvec and .bval files. It's not that the tags do...
import nibabel as nib import nibabel.processing from nilearn.image import resample_img img = nib.load('./dicom_to_nifti.nii') new_img = nibabel.processing.resample_to_output(img, (2, 2, 2)) new_img.to_filename('nifti_2_2_2') However I keep getting this error that says that it ...
I use the dicom2nifti package to first create a nifti file from the folder containing DICOM files and then I use nibabel to open the created nifti file. THEN I get affine info with nii.affine (where nii is the loaded nifti file python object). This is why, the creation of the nifti...
DICOM is not supported in OpenCV, see here. You will have to convert all of your images into a suitable format (e.g. jpg or png) before you are able to resize them with OpenCV: OpenCV does not support DICOM images so that you will have to find a suitable libary (like http://di...
SimpleITK manifest.json file help adding new NIFTI file I am using SimpleITK for image registration purposes. I followed the tutorials and would like to run the program on other brain MRI's now that were not provided in the tutorial. I know I have to add ... ...
I needed to reorient NIfTI images (files with .nii or .nii.gz extension) and the above solution didn't work for me. After some research in the SimpleITK library I found the function sitk.DICOMOrient() which worked for me. Adjusting to your example (Tested in version 2.1.1 of SimpleITK...
Could someone explain the output of SimpleITK.GetDirection() and how is related to DICOM standard Image Orientation (Patient) header and NIFTI? Eventually, I would like to get the right Image Orientation (Patient) given a cut e.g. axial, sagittal, coronal. I am aware of the example, https...
2 Reading a dicom file in C 0 Cocoa app with ITK, VTK to read DICOM file 1 How to save a DICOM series raw with VTK 0 Read DICOM images 0 How can I parse a DICOM file using plain C or C++ file read methods? 2 Convert DICOM image using VTK 3 DCMTK C++ : how to ...
0 Medical Imaging Data - how to convert .raw/mhd to Nifti/nii 1 How to get affine information from a DICOM file in python? 2 How to check NIFTI image is in the right orientation/position with Python 3 Conversion not working properly using dicom2nifti Hot...