FSL FLIRT '-omat' affine matrix output not in decimal format

zmorrissey commented 5 years ago

Summary

Hello, I am using the nipype.interfaces.fsl.FLIRT() command to register a T2 atlas nifti image to a T2 subject nifti image, and I need the affine matrix output of this transformation for the following step to transform the atlas labels into the subject space.

After running the FSL interface's FLIRT command using the out_matrix_file input, it appears to run successfully without any errors, but the resulting .mat file appears to be in a hex type of format instead of decimal format, and there don't appear to be any options listed in the documentation to specify the format for this output file. However, if I run the same command directly in bash, the affine matrix appears (normal) in decimal format.

I'm not sure if this due to nipype or if there is a way to check which version of FSL nipype is calling? I had a similar issue using bash with an earlier version of FSL that was fixed after upgrading to FSL 6.0.

Any help would be appreciated. Thank you!

Actual behavior

The result of nipype's FLIRT out_matrix_file option is a .mat file that is not in recognizable decimal format:

0x1.f3704b5f9a7a8p-1  -0x1.7233534569a2ap-5  0x1.b8452355d1391p-9  0x1.46384be3f5eacp+2  
0x1.71392a592f9f9p-5  0x1.f4bb310ffd381p-1  0x1.609369afdb69fp-11  -0x1.3f0114ec4ce68p+0  
-0x1.d43cafec304ap-9  -0x1.78c17ac5694fep-11  0x1.f64664aad24ecp-1  -0x1.0b85d4efb3e03p+2  
0x0p+0  0x0p+0  0x0p+0  0x1p+0

Expected behavior

When I run the same command in bash using flirt, I get this matrix:

0.9754661135  -0.04519048942  0.003358994068  5.097186062  
0.04507120391  0.977990659  0.00067248503  -1.246110256  
-0.00357236526  -0.0007186046211  0.9810058077  -4.180043444  
0  0  0  1

Script/Workflow details

In Python:

from nipype.interfaces.fsl import FLIRT

flt = FLIRT()
flt.inputs.in_file = 't2_atlas.nii.gz'
flt.inputs.reference = 'subject01_t2.nii.gz'
flt.inputs.out_file = 'atlas_in_t2_space.nii.gz'
flt.inputs.output_type = 'NIFTI_GZ'
flt.inputs.out_matrix_file = 'TM_atlas_to_t2.mat'
flt.run()

If I take the flt.cmdline output and run it directly in bash, it works properly:

flirt -in t2_atlas.nii.gz -ref subject01_t2.nii.gz -out atlas_in_t2_space.nii.gz -omat TM_atlas_to_t2.mat

Platform details:

{'commit_hash': 'b448b6061',
 'commit_source': 'installation',
 'networkx_version': '2.1',
 'nibabel_version': '2.3.1',
 'nipype_version': '1.1.6',
 'numpy_version': '1.14.2',
 'pkg_path': '/usr/local/lib/python3.5/dist-packages/nipype',
 'scipy_version': '1.0.0',
 'sys_executable': '/usr/bin/python3',
 'sys_platform': 'linux',
 'sys_version': '3.5.2 (default, Nov 23 2017, 16:37:01) \n[GCC 5.4.0 20160609]',
 'traits_version': '4.6.0'}

Execution environment

Ubuntu 16.04 xenial Python 3.5.2 ipython v6.4.0 nipype v1.5.6 fsl v6.0.0

satra commented 5 years ago

this is really weird because nipype doesn't write the file, fsl does. are you running the nipype command and the bash version in the same terminal (just to rule out environment issues).

zmorrissey commented 5 years ago

@satra,

Thanks for the reply. I tried your suggestion, and started a new ipython session directly in the terminal and ran the same nipype commands. Looks like it is working normally this way, I was able to get a decimal format .mat file like I did when running regular fsl.

I have been running my nipype code in an ipython session in Emacs v25.3.2; since it is working properly via the terminal perhaps this an environment issue?

satra commented 5 years ago

@zmorrissey - seems like it. you may want to compare the environment variables inside emacs ipython and on the terminal. it may have something with language and encoding settings.

zmorrissey commented 5 years ago

@satra - I see, I will look into this to see if I can hunt down which environment variables are causing the issue in case others have similar problems. I appreciate your help and prompt reply!

Thank you.

nipy / nipype