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Questions tagged [nifti]

A data format used in biomedical imaging, proposed by the Neuroimaging Informatics Technology Initiative.

It can be used to represent the 2 current formats, NIfTI-1 or NIfTI-2, as well as the organization behind it, the Neuroimaging Informatics Technology Initiative.

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Which version of `gcc` supports the `--no-undefined` switch?

I am trying to compile pynifti package from source (long story involving Anaconda Python distribution). After running make, I receive the following error: gcc: error: unrecognized command line option ‘--Wl,--no-undefined’ Indeed, the manual (man…
abukaj
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writeNIfTI failure - Error in if (!all(object@dim_[indices] > 0 & pixdim(object)[indices] > : missing value where TRUE/FALSE needed

I am trying to write out a NIfTI file I created from DICOM images. For this example I am using a DICOM image from Kaggle's Data Science Bowl. You have to accept the terms to download the example file, but it can be found here in the "stage1"…
Hack-R
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Execute nii2mnc in matlab

I am trying to make a script in MATLAB that runs also some commands. Everything works fine so far except from the nii2mnc. I am getting different results when i run it in cmd and when i run it through my script in MATLAB. At first the problem was…
Christos ZS
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Failed to read DICOM files in C++ ITK after conversion from .nii format

I converted NifTi (.nii) dataset into DICOM dataset using the plugin Tudor DICOM from ImageJ. The generated files work fine with ImageJ but are not accepted from ITK. I become these warnings: function gdcm::DataSet::GetMediaStorage Media Storage…
Fliss
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Is it possible to convert 3D Matlab figure into .mat?

Actually I have .fig file and want to convert it into nifti file (.nii), then I found make_nii function which request a .mat file.
sahbi.m
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Is it possible to assign a variable to a dimension in a 3D array?

The size of my 3D array is (20, 33, 20). What I would like to do is to run a loop where, for instance, if there is a 0 in the 1st column (20), then the loop would go back to find a number that is non zero, then have the loop advance to the 2nd…
aaa905
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VTK - How to read Tensors/Matrix per cell from a NIFTI Image?

I'm trying to implement a MRT-DTI real-time fibertracking visualization tool based on VTK. Therefore we need to read the DTI tensors/matrices per cell stored in a NIFTI Image (.nii) and I really can't figure out how to do this. It's not a problem to…
hausfrau87
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Creating a 3D wireframe cortical model from MNI brain template with Matlab using MyRobustCrust

I am attempting to create a wireframe 3d model from an MNI brain template using MyRobustCrust on matlab. My goal is to be able to determine MNI coordinates on the cortical surface. To do this, I'm following the instructions listed at this site:…
Green_Crim
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How to transfer Nifti file into .mat Matlab file?

I have a Nifti file, the size of which is 62*62*38. How can I transfer the Nifti file to .mat Matlab file?
Angelababy
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How to display NIFTI image that is read using vtkNIFTIImageReader with VTK

I can display sliced images using vtkNIFTIImageReader with the following code : https://github.com/dgobbi/vtk-dicom/blob/master/Examples/TestNIFTIDisplay.cxx However, when I try to render the NIFTI file as a 3D object, it always comes up empty. How…
user2816456
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How to upload nifti images

I have a folder with files that have the format .nii.gz. How can I upload these images in Python? Should I create a for loop ? Any help please
chris
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Python DICOM--pixel dimension

I beginner in DICOM file, how to find pixel dimension or dim in these files? As we find these elements in the nifti files!
leila mm
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Imaging: Replaces values by 0 over specific threshold

I have data of type float64 which has the size (57, 66, 40). I want to replace all values smaller than 0.9 by 0. I tried the easiest way without a loop: img = nib.load('/home/anja/aw.nii') data = img.get_fdata() threshold_data = data[data<0.9] ==…
Anja
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Align two NIFTI files with different origins and sizes?

I have two fMRI NIFTI (.nii) files (a region of interest (ROI) mask and an SPM T-contrast), both of which I can read into Matlab using load_nii, giving me two structures. The actual image data within these structures are different sizes and oriented…
Dylan Royston
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