bvec and bval extraction from dti sequences

leej3 commented 7 years ago

Summary

bval and bvec files are not kept during a conversion of certain dti dicoms using the dcm2niix interface. From what I can tell this might be due the appropriate pattern not being found in the stdout of dcm2niix. This search is performed on line 307 of the dcm2nii.py interface file :

elif 'DTI gradients' in line or 'DTI gradient directions' in line: find_b = True

(https://github.com/nipy/nipype/blob/master/nipype/interfaces/dcm2nii.py, af2b7aaa60a9ab28116c0edb019a2e34c959b3d4)

Actual behavior

Using nipype to convert from dicom to nifti, both .nii.gz. and .json files are retrieved but the bvec and bval files are deleted during the post conversion clean up.

Expected behavior

DTI sequence dicoms yield nifti, json, bvec, and bval given the appropriate conversion flags

How to replicate the behavior

I can't share the DICOM, it was collected recently on a GE scanner (DISCOVERY MR750).

Script/Workflow details

base_dir = '/data/troubleshooting_dti_failure/'
%cd {base_dir}

/data/troubleshooting_dti_failure

Dcm2niix

mkdir dcm2niix_output

tar_list = !tar xvf dti_test_dicoms_001_001.tar.gz
tar_list[:5]

['dti_dicoms/',
 'dti_dicoms/mr_0017/',
 'dti_dicoms/mr_0017/edti_2mm_cdif99-00073.dcm',
 'dti_dicoms/mr_0017/edti_2mm_cdif99-00163.dcm',
 'dti_dicoms/mr_0017/edti_2mm_cdif99-00087.dcm']

ls

[0m[01;34mdcm2niix_output[0m/  [01;34mdti_dicoms[0m/  [01;32mdti_test_dicoms_001_001.tar.gz[0m*

!dcm2niix -b y -z i -x n -t n -m n -f dwi -o /data/troubleshooting_dti_failure/dcm2niix_output \
-s n -v n /data/troubleshooting_dti_failure/dti_dicoms/mr_0013/edti_2mm_cdif09_g01-00001.dcm

Compression will be faster with /usr/local/bin/pigz
Chris Rorden's dcm2niiX version v1.0.20170314 (64-bit Linux)
Found 1680 DICOM image(s)
Reorienting edti_2mm_cdif09_G01 : 20 GE DTI vectors: please validate. isCol=1 sliceDir=3 flp=0 0 1
Convert 1680 DICOM as /data/troubleshooting_dti_failure/dcm2niix_output/dwi (128x128x84x20)
Conversion required 2.709230 seconds.

ls dcm2niix_output/

dwi.bval  dwi.bvec  dwi.json  dwi.nii.gz

Nipype

from nipype import __version__
__version__

u'0.13.0-dev'

from nipype import Function, Node
from nipype.interfaces.base import isdefined
from nipype.interfaces.dcm2nii import Dcm2nii, Dcm2niix
import os

%cd {base_dir}
tmpdir = '/data/troubleshooting_dti_failure/nipype_dicoms'
%rm -rf {tmpdir}

%mkdir {tmpdir}
!cp -R dti_dicoms/mr_0013/* {tmpdir}
%cd {tmpdir}

/data/troubleshooting_dti_failure
/data/troubleshooting_dti_failure/nipype_dicoms

# need to be abspaths!
dicoms = list(map(os.path.abspath, os.listdir('.')))
dicoms[:5]

['/data/troubleshooting_dti_failure/nipype_dicoms/edti_2mm_cdif09_g01-01440.dcm',
 '/data/troubleshooting_dti_failure/nipype_dicoms/edti_2mm_cdif09_g01-00974.dcm',
 '/data/troubleshooting_dti_failure/nipype_dicoms/edti_2mm_cdif09_g01-00793.dcm',
 '/data/troubleshooting_dti_failure/nipype_dicoms/edti_2mm_cdif09_g01-01367.dcm',
 '/data/troubleshooting_dti_failure/nipype_dicoms/edti_2mm_cdif09_g01-00909.dcm']

converter = 'dcm2niix'
prefix_name = 'dwi'
convertnode = Node(Dcm2niix(), name='convert')
convertnode.base_dir = os.path.abspath(tmpdir)
convertnode.inputs.source_names = dicoms
convertnode.inputs.out_filename = 'dwi'
convertnode.inputs.terminal_output = 'allatonce'

res = convertnode.run()

170705-20:08:48,121 workflow INFO:
     Executing node convert in dir: /data/troubleshooting_dti_failure/nipype_dicoms/convert
170705-20:08:48,853 workflow INFO:
     Running: dcm2niix -b y -z i -x n -t n -m n -f dwi -o /data/troubleshooting_dti_failure/nipype_dicoms/convert -s n -v n /data/troubleshooting_dti_failure/nipype_dicoms/convert/edti_2mm_cdif09_g01-01440.dcm

res.outputs

bids = /data/troubleshooting_dti_failure/nipype_dicoms/convert/dwi.json
bvals = <undefined>
bvecs = <undefined>
converted_files = /data/troubleshooting_dti_failure/nipype_dicoms/convert/dwi.nii.gz

Please put URL to code or code here (if not too long). https://github.com/leej3/dti_conversion_issue

Platform details:

Please paste the output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"

The above command doesn't working (its python 2 in the container). NiPipye : 0.13.0-dev Python : 2.7 Nibabel: 2.1.0

Execution environment

Running inside the nipy/heudiconv image: sha256:8b3b92bb63ac72ced5f2f92bd9e6c9312a98ef6b503ba53f29d4623d3f8fa8e1

mgxd commented 7 years ago

@leej3 thanks for pointing this out - this interface was only tested with Siemens dicoms.

looks like the fix should be pretty straightforward - adding a search for GE DTI vectors when parsing the stdout - could you give it a try? And if it works, could you submit a PR?

EDIT: read my mind!

leej3 commented 7 years ago

Ah, you spotted it. Great. The change has worked for me so far.

Cheers

nipy / nipype