Issues of interfacing with PETPVC modules

[ubersexualShupeng]

Hi @effigies @alexsavio, I have run it in a Node and the content of the file report.rst as following:

Node: petpvc

Hierarchy : pvc
Exec ID : pvc

Original Inputs

• alpha :
• args :
• debug : False
• environ : {}
• fwhm_x : 2.0
• fwhm_y : 2.0
• fwhm_z : 2.0
• ignore_exception : False
• in_file : C:\Users\135173\Desktop\pvc_test\PET_nii\x_WB_CTAC_Body.nii.gz
• mask_file : C:\Users\135173\Desktop\pvc_test\mask_nill\skin_mask.nii.gz
• n_deconv :
• n_iter :
• out_file : C:\Users\135173\Desktop\pvc_test\pet_pvc_rbv.nii.gz
• pvc : RBV
• stop_crit :
• terminal_output : stream

Thanks.

[effigies]

I don't see a problem with your environment. I wonder if you're not escaping the back slashes in the file paths.

…

On Jun 6, 2017 11:54, "ubersexualShupeng" ***@***.***> wrote: Hi @effigies <https://github.com/effigies> @alexsavio <https://github.com/alexsavio>, I have run it in a Node and the content of the file report.rst as following: Node: petpvc Hierarchy : pvc Exec ID : pvc Original Inputs - alpha : - args : - debug : False - environ : {} - fwhm_x : 2.0 - fwhm_y : 2.0 - fwhm_z : 2.0 - ignore_exception : False - in_file : C:\Users\135173\Desktop\pvc_test\PET_nii\x_WB_CTAC_Body. nii.gz - mask_file : C:\Users\135173\Desktop\pvc_test\mask_nill\skin_mask.nii. gz - n_deconv : - n_iter : - out_file : C:\Users\135173\Desktop\pvc_test\pet_pvc_rbv.nii.gz - pvc : RBV - stop_crit : - terminal_output : stream Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2068>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFF8k0GOZhFXLcECocy2KO5litwNfSmks5sBXY-gaJpZM4NxjRB> .

[ubersexualShupeng]

I have tried to replace the back slashes to 'double back slashes' '\' or forward dash '/' but the same error still appeared. Is there are any other possible problems?

The error messages as following:
TypeError: environment can only contain strings
Interface PETPVC failed to run.

Thanks.

[effigies]

I believe nipype will pass your actual environment through. Can you check

import os
print(os.environ)

for non-string keys/values? (This may contain some personal information. If you're going to post the results of this for inspection, consider censoring it.)

[mgxd]

@ubersexualShupeng are you still running into this issue?

[ubersexualShupeng]

Yes. I do not use this py module anymore. I use the PETPVC (binary) directly now.

[effigies]

To be clear, are you able to run other external programs, such as FSL or FreeSurfer, through nipype, or is this TypeError specifically for PETPVC?

---

To get the context in this issue, the code run was:

import nipype
import nipype.interfaces.petpvc as PETPVC
pvc = PETPVC.PETPVC()
pvc.inputs.in_file = 'C:\Users\135173\Desktop\pvc_test\PET_nii\x_WB_CTAC_Body.nii.gz'
pvc.inputs.mask_file = 'C:\Users\135173\Desktop\pvc_test\mask_nill\skin_mask.nii.gz'
pvc.inputs.out_file = 'C:\Users\135173\Desktop\pvc_test\pet_pvc_rbv.nii.gz'
pvc.inputs.pvc = 'RBV'
pvc.inputs.fwhm_x = 2
pvc.inputs.fwhm_y = 2
pvc.inputs.fwhm_z = 2
outs = pvc.run()

With error:

 Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Program Files\Anaconda2\lib\site-packages\nipype\interfaces\base.py", line 1081, in run
    runtime = self._run_wrapper(runtime)
  File "C:\Program Files\Anaconda2\lib\site-packages\nipype\interfaces\base.py", line 1724, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "C:\Program Files\Anaconda2\lib\site-packages\nipype\interfaces\base.py", line 1755, in _run_interface
    redirect_x=self._redirect_x)
  File "C:\Program Files\Anaconda2\lib\site-packages\nipype\interfaces\base.py", line 1457, in run_command
    env=runtime.environ)
  File "C:\Program Files\Anaconda2\lib\subprocess.py", line 390, in __init__
    errread, errwrite)
  File "C:\Program Files\Anaconda2\lib\subprocess.py", line 640, in _execute_child
    startupinfo)
TypeError: environment can only contain strings
Interface PETPVC failed to run.

This may be a Unicode-on-Windows issue (see https://stackoverflow.com/questions/12253014/why-does-popen-fail-on-windows-if-the-env-parameter-contains-a-unicode-object).

I can see if I can make a patch that filters the environment for unicode strings and replaces them with bytes.

[effigies]

Hi @ubersexualShupeng. Can you give #2085 a shot?

pip install --upgrade "git+https://github.com/effigies/nipype.git@fix/windows_env#egg=nipype"