Runtime error (invalid literal for int() with base 10: 'Mask and image must be the same size') during ICA-AROMA, fMRIprep 1.0.0-rc8

1

Hi,

I am trying to run fMRIprep (v. 1.0.0-rc8) with ICA-AROMA and am getting the following error:

Node: fmriprep_wf.single_subject_105_wf.func_preproc_task_future_run_01_wf.bold_confounds_wf.ica_aroma_wf.ica_aroma
Working directory: /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/ica_aroma

Node inputs:

TR = <undefined>
args = <undefined>
compress_report = auto
denoise_type = nonaggr
dim = <undefined>
environ = {}
feat_dir = <undefined>
fnirt_warp_file = <undefined>
generate_report = True
ignore_exception = False
in_file = /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz
mask = <undefined>
mat_file = <undefined>
melodic_dir = /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/melodic
motion_parameters = /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_hmc_wf/normalize_motion/motion_params.txt
out_dir = <undefined>
out_report = ica_aroma_reportlet.svg
report_mask = /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_mni_trans_wf/mask_mni_tfm/ref_image_corrected_trans_masked_corrected_brain_mask_maths_trans.nii.gz
terminal_output = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 407, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 517, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1088, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/common/report.py", line 55, in _run_interface
    ReportCapableInterface, self)._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1654, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1600, in raise_exception
    **runtime.dictcopy()))
RuntimeError: Command:
ICA_AROMA.py -den nonaggr -i /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz -meldir /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/melodic -mc /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /root/src/fmriprep/work/fmriprep_wf/single_subject_105_wf/func_preproc_task_future_run_01_wf/bold_confounds_wf/ica_aroma_wf/ica_aroma
Standard output:

------------------------------- RUNNING ICA-AROMA ------------------------------- 
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' --------------- 

Step 1) MELODIC
  - The existing/specified MELODIC directory will be used.
  - The MELODIC directory does not contain the required 'stats' folder. Mixture modeling on the Z-statistical maps will be run.
Step 2) Automatic classification of the components
  - registering the spatial maps to MNI
  - extracting the CSF & Edge fraction features
Standard error:
Traceback (most recent call last):
  File "/opt/ICA-AROMA/ICA_AROMA.py", line 200, in <module>
    edgeFract, csfFract = aromafunc.feature_spatial(fslDir, outDir, scriptDir, melIC_MNI)
  File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 388, in feature_spatial
    '-V | awk \'{print $1}\''])))
ValueError: invalid literal for int() with base 10: 'Mask and image must be the same size'
Return code: 1

Any ideas what’s wrong? Please let me know if I can provide any additional information about the error, I just don’t know exactly what to check.

Thanks,
Kristina

2

I’m assuming that the other post (FreeSurfer license file error in fMRIprep 1.0.0-rc10) was a result of trying to upgrade to see if that fixes the problem? If so, that would be my first suggestion, to make sure that this issue hasn’t been fixed.

3

I am still getting the same error in newer versions. I tried all the way up to 1.0.0-rc12. Any idea what I could look at to find out what’s going on?

4

Hi @kwiebels, you are right - looking at the inputs it seems I made a mistake when I refactored the confounds workflow. I’ve opened https://github.com/poldracklab/fmriprep/issues/870 and try to have a look ASAP.

Volunteers, of course, are always welcome.

5

Thanks @oesteban. I would love to help, but unfortunately I don’t have the technical skills at all. Let me know if there is anything a little noob can do.

Thanks so much to you and the team for developing such great tools!

6

Hi,

We are struggling to replicate this on our data. Could you try out this solution? https://github.com/poldracklab/fmriprep/pull/1064#issuecomment-383314377

7

Hi @kwiebels, are you still interested in running your data through ICA-AROMA? If so, could you please give a try to poldracklab/fmriprep:1.0.12-dev0?

Thanks!

8

Hey,

yes, I am. I’ll try that and will report back soon.

Thanks, @oesteban and @ChrisGorgolewski

9

Sorry for the late reply. We had some technical issues with our computing resources (unrelated). But it finally got resolved now and using poldracklab/fmriprep:1.0.12-dev0 worked perfectly!

2 Likes
10

The error message invalid literal for int() with base 10 would seem to indicate that you are passing a string that’s not an integer to the int() function . In other words it’s either empty, or has a character in it other than a digit. You can solve this error by using Python isdigit() method to check whether the value is number or not. The returns True if all the characters are digits, otherwise False .

if val.isdigit():

The other way to overcome this issue is to wrap your code inside a Python try…except block to handle this error.

Python2.x and Python3.x

Sometimes the difference between Python2.x and Python3.x that leads to this ValueError: invalid literal for int() with base 10 . With Python2.x , int(str(3/2)) gives you “1”. With Python3.x , the same gives you (“1.5”): ValueError: invalid literal for int() with base 10: “1.5”.