Error while running GradQC

nabin · October 1, 2019, 9:11pm

Dear Slicer team,

I am trying to run the module GradQC to check the quality of my diffusion data and it’s supposed to be a simple process which should work by giving input as my dwi.nii.gz file and run it but it throws an error as follow. Your support will be highly appreciated.
Thank you.
Nabin

Error:

diffusionQC standard error:

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/Slicer-4.10/cli-modules/diffusionQC.py”, line 57, in
QC.run()
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/plumbum/cli/application.py”, line 572, in run
retcode = inst.main(*tailargs)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/Slicer-4.10/cli-modules/diffusionQC.py”, line 53, in main
process(self.dwi, self.mask, self.out, self.autoMode)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/diffusionqclib/gradient_process.py”, line 197, in process
hdr, mri, grad_axis, slice_axis, b_value, gradients = dwi_attributes(dwiPath)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/diffusionqclib/dwi_attributes.py”, line 8, in dwi_attributes
dwi= nrrd.read(file_name)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/nrrd/reader.py”, line 503, in read
header = read_header(fh, custom_field_map)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/nrrd/reader.py”, line 247, in read_header
header_size += _validate_magic_line(magic_line)
File “/Applications/Slicer.app/Contents/Extensions-28257/DiffusionQC/lib/python2.7/site-packages/nrrd/reader.py”, line 183, in _validate_magic_line
raise NRRDError(‘Invalid NRRD magic line. Is this an NRRD file?’)
nrrd.errors.NRRDError: Invalid NRRD magic line. Is this an NRRD file?

tbillah · October 2, 2019, 2:43am

Hi @nabin,

Our tool is NRRD only. As you might already know, Slicer can load only NRRD 4D image, not NIFTI 4D image.

For future reference, here is the Tutorial for GradQC:

However, you can use my NIFTI–>NRRD conversion tool, obtain an NHDR for the NIFTI image you are trying to GradQC and then load the NHDR header seamlessly to perform GradQC on it.

github.com

pnlbwh/conversion/blob/master/conversion/nhdr_write.py

#!/usr/bin/env python

import numpy as np
import argparse
import os, warnings, sys
# with warnings.catch_warnings():
#     warnings.filterwarnings("ignore", category=FutureWarning)
import nibabel as nib

PRECISION= 17
np.set_printoptions(precision= PRECISION, suppress= True, floatmode= 'maxprec')

from conversion.bval_bvec_io import read_bvecs, read_bvals, bvec_scaling

def matrix_string(A):
    # A= np.array(A)
    
    A= str(A.tolist())
    A= A.replace(', ',',')
    A= A.replace('],[',') (')

This file has been truncated. show original

Let me know if you need more help.

-Tashrif

nabin · October 2, 2019, 12:45pm

Thanks a lot Tashrif. I will try with this converting it to nrrd format.

Best,

Nabin

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Error while running GradQC

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