Matlab command cannot be found

[jykim24]

Summary

Hello, I'm new to nipype and I am following preprocessing tutorial in the NypypeBeginnersGuide, and I cannot seem to run the workflow or write a graph.
The workflow unzips the file, but crashes at slice timing.
The crash file created states that matlab command cannot be found, but I have matlab 2016b and SPM12 installed.
Also, the error tells that 'No command 'dot' found' when I try to write a graph.

When testing nipype with nipype.test(), a fauilure occurs in test_Commandline().
I've deleted and reinstalled nipype twice, but this problem occurred both times.

How can I resolve these issues?

Actual behavior

When trying to write a graph,

OSError Traceback (most recent call last)
in ()
1 # 7. run workflow
----> 2 pp.write_graph(graph2use='flat')

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py in write_graph(self, dotfilename, graph2use, format, simple_form)
448 dotfilename=dotfilename,
449 format=format,
--> 450 simple_form=simple_form)
451
452 logger.info(

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py in export_graph(graph_in, base_dir, show, use_execgraph, show_connectinfo, dotfilename, format, simple_form)
1285
1286 # Convert .dot if format != 'dot'
-> 1287 outfname, res = _run_dot(out_dot, format_ext=format)
1288 if res is not None and res.runtime.returncode:
1289 logger.warning('dot2png: %s', res.runtime.stderr)

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py in _run_dot(dotfilename, format_ext)
1328 cmd = 'dot -T{} -o"{}" "{}"'.format(format_ext, formatted_dot, dotfilename)
1329 res = CommandLine(cmd, terminal_output='allatonce',
-> 1330 resource_monitor=False).run()
1331 return formatted_dot, res
1332

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py in run(self, cwd, **inputs)
513
514 try:
--> 515 runtime = self._run_interface(runtime)
516 outputs = self.aggregate_outputs(runtime)
517 except Exception as e:

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py in _run_interface(self, runtime, correct_return_codes)
1011 'No command "%s" found on host %s. Please check that the '
1012 'corresponding package is installed.' % (executable_name,
-> 1013 runtime.hostname))
1014
1015 runtime.command_path = cmd_path

OSError: No command "dot" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.

When trying to run the workflow,

180212-11:06:51,706 workflow INFO:
Workflow preprocessing settings: ['check', 'execution', 'logging', 'monitoring']
180212-11:06:51,759 workflow INFO:
Running serially.
180212-11:06:51,763 workflow INFO:
[Node] Setting-up "preprocessing.selectfiles" in "/Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/wd_preprocessing/preprocessing/_session_id_run001_subject_id_sub002/selectfiles".
180212-11:06:51,785 workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180212-11:06:51,823 workflow INFO:
[Node] Finished "preprocessing.selectfiles".
180212-11:06:51,825 workflow INFO:
[Node] Setting-up "preprocessing.gunzip" in "/Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/wd_preprocessing/preprocessing/_session_id_run001_subject_id_sub002/gunzip".
180212-11:06:51,834 workflow INFO:
[Node] Cached "preprocessing.gunzip" - collecting precomputed outputs
180212-11:06:51,841 workflow INFO:
[Node] "preprocessing.gunzip" found cached.
180212-11:06:51,845 workflow INFO:
[Node] Setting-up "preprocessing.slice_timing" in "/Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/wd_preprocessing/preprocessing/_session_id_run001_subject_id_sub002/slice_timing".
180212-11:06:51,898 workflow INFO:
[Node] Running "slice_timing" ("nipype.interfaces.spm.preprocess.SliceTiming")
180212-11:06:51,923 workflow WARNING:
[Node] Error on "preprocessing.slice_timing" (/Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/wd_preprocessing/preprocessing/_session_id_run001_subject_id_sub002/slice_timing)
180212-11:06:51,929 workflow ERROR:
Node slice_timing.a1 failed to run on host Juyoungs-MacBook-Pro.local.
180212-11:06:51,972 workflow ERROR:
Saving crash info to /Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/crash-20180212-110651-juyoungkim-slice_timing.a1-bffe58c0-53dd-4946-abe8-a60895ad07c9.pklz
Traceback (most recent call last):
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
result = self._run_interface(execute=True)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return self._run_command(execute)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run(cwd=outdir)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 515, in run
runtime = self._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/spm/base.py", line 359, in _run_interface
results = self.mlab.run()
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 515, in run
runtime = self._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/matlab.py", line 162, in _run_interface
runtime = super(MatlabCommand, self)._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1013, in _run_interface
runtime.hostname))
OSError: No command "matlab" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.

Crash file states,
1_subject_id_sub001/slice_timing

Node inputs:

ignore_exception = False
in_files = ['/Users/juyoungkim/D_drive/spm_study_1702/spm_practice/nipype_tutorial/wd_preprocessing/preprocessing/_session_id_run001_subj
ect_id_sub001/slice_timing/run001.nii']
matlab_cmd =
mfile = True
num_slices = 40
out_prefix = a
paths =
ref_slice = 2
slice_order = [1.0, 3.0, 5.0, 7.0, 9.0, 11.0, 13.0, 15.0, 17.0, 19.0, 21.0, 23.0, 25.0, 27.0, 29.0, 31.0, 33.0, 35.0, 37.0, 39.0, 2.0, 4.
0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0, 18.0, 20.0, 22.0, 24.0, 26.0, 28.0, 30.0, 32.0, 34.0, 36.0, 38.0, 40.0]
time_acquisition = 1.95
time_repetition = 2.0
use_mcr =
use_v8struct = True

Traceback:
Traceback (most recent call last):
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
result = self._run_interface(execute=True)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
return self._run_command(execute)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run(cwd=outdir)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 515, in run
runtime = self._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/spm/base.py", line 359, in _run_interface
results = self.mlab.run()
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 515, in run
runtime = self._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/matlab.py", line 162, in _run_interface
runtime = super(MatlabCommand, self)._run_interface(runtime)
File "/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1013, in _run_interface
runtime.hostname))
OSError: No command "matlab" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.

Expected behavior

Write a graph and run the preprocessing workflow.

How to replicate the behavior

Script/Workflow details

Please put URL to code or code here (if not too long).

Platform details:

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

Execution environment

I'm running on Jupyter notebook, on Mac os, and have Nipype 1.0, MATLAB2016b and SPM12 installed.

Choose one

• Container [Tag: ???]
• My python environment inside container [Base Tag: ???]
• My python environment outside container

[djarecka]

@jykim24 - you mentioned several issues here, will try to address at least some of them:

• re. dot: write_graph function used in Nipypes requires a software called graphviz, I know there are some issues on OSX, as far as I remember brew install graphviz helped in my case. You can always check if you have dot in your terminal dot -V. FYI: you don't need dot to run the nipype workflow.

• re spm: can you check what is the output python -c "from nipype.interfaces import spm; print(spm.Info.name())"?

• re failing test: can you please share what is the failure message that you get from test_Commandline()

• general comment: I'm not sure if NipypeBeginnersGuide has been updated recently (@miykael will know more) and don't know which example you're trying to run, but you can also check nipype tutorial that has been recently updated and tested.

[jykim24]

@djarecka
Thanks so much for the prompt reply!
I have been following the same tutorial on the link, using the flanker task dataset.

1. dot: I didn't know dot is not mandatory to run the workflow. I haven't tried the command yet, but I will. Thanks for the tip!

2. spm: the output of the code line says 'None', but I have SPM12 installed, and it's added to path in my MATLAB.

3. test failure message:

=================================================================== FAILURES ====================================================================
____________________________________________________________ test_CommandLine_output ____________________________________________________________

tmpdir = local('/private/var/folders/nf/6my3rs5d7kx9rvdr2jg72wsr0000gn/T/pytest-of-juyoungkim/pytest-26/test_CommandLine_output0')

def test_CommandLine_output(tmpdir):
    # Create one file
    tmpdir.chdir()
    file = tmpdir.join('foo.txt')
    file.write('123456\n')
    name = os.path.basename(file.strpath)

    ci = nib.CommandLine(command='ls -l')
    ci.terminal_output = 'allatonce'
    res = ci.run()
    assert res.runtime.merged == ''
    assert name in res.runtime.stdout

    # Check stdout is written
    ci = nib.CommandLine(command='ls -l')
    ci.terminal_output = 'file_stdout'
    res = ci.run()
    assert os.path.isfile('stdout.nipype')
    assert name in res.runtime.stdout
    tmpdir.join('stdout.nipype').remove(ignore_errors=True)

    # Check stderr is written
    ci = nib.CommandLine(command='ls -l')
    ci.terminal_output = 'file_stderr'
    res = ci.run()
    assert os.path.isfile('stderr.nipype')
    tmpdir.join('stderr.nipype').remove(ignore_errors=True)

    # Check outputs are thrown away
    ci = nib.CommandLine(command='ls -l')
    ci.terminal_output = 'none'
    res = ci.run()
    assert res.runtime.stdout == '' and \
        res.runtime.stderr == '' and \
        res.runtime.merged == ''

    # Check that new interfaces are set to default 'stream'
    ci = nib.CommandLine(command='ls -l')
    res = ci.run()

  assert ci.terminal_output == 'stream'

E AssertionError: assert 'file' == 'stream'
E - file
E + stream

/Users/juyoungkim/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/tests/test_core.py:441: AssertionError
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=============================================== 1 failed, 635 passed, 5 skipped in 29.46 seconds ================================================

[djarecka]

re 2: let's try to set the path manually, you can check python -c "from nipype.interfaces import spm; spm.SPMCommand.set_mlab_paths(paths='/your/path/to/spm'); print(spm.Info.name())"

If this helps, you can add spm.SPMCommand.set_mlab_paths at the beginning of the script to help nipype to find your spm.

[jykim24]

I've tried, but 'print(spm.Info.name())' still gives 'None'.
SPM runs just fine on Matlab, though.

[jykim24]

@djarecka
I've also tried to add path to .bash_profile but it didn't work either.

from nipype.interfaces import spm
from nipype import config, logging
config.enable_debug_mode()
logging.update_logging(config)
spm.SPMCommand.set_mlab_paths(paths='/Applications/MATLAB_R2016b/toolbox/spm12/')
print(spm.Info.name())
print(spm.SPMCommand().version)

above lines give me the following messages:

180212-19:58:09,71 interface DEBUG:
nodesktop_True
180212-19:58:09,75 interface DEBUG:
nosplash_True
180212-19:58:09,89 interface DEBUG:
single_comp_thread_True
180212-19:58:09,95 interface DEBUG:
No command "matlab" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.
None
180212-19:58:09,104 interface DEBUG:
nodesktop_True
180212-19:58:09,117 interface DEBUG:
nosplash_True
180212-19:58:09,122 interface DEBUG:
single_comp_thread_True
180212-19:58:09,133 interface DEBUG:
No command "matlab" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.
None

It seems I can't run matlab from nipype, and that's causing the problems.
Is there something I can try?

Thanks in advance!

[djarecka]

can you try spm.SPMCommand.set_mlab_paths(paths='/your/path/to/spm', matlab_cmd='/path/to/matlab -nodesktop -nosplash') instead of spm.SPMCommand.set_mlab_paths(paths='/your/path/to/spm')

[djarecka]

@jykim24 - can ask you to create a separate issue for the failing test? It doesn't seem to be related to your problems with spm and the tutorial. I personally never seen it and can't reproduce it, other people might have better ideas when they see it.

[jykim24]

@djarecka

Sure, I will create a separate issue for test failure.
For your suggested solution, I've tried running the following code.

from nipype.interfaces import matlab
from nipype.interfaces import spm
spm.SPMCommand.set_mlab_paths(paths='/Applications/MATLAB_R2016b.app/toolbox/spm12/')
matlab_cmd='/Applications/MATLAB_R2016b -nodesktop -nosplash'
print(spm.Info.name())

When I run the code, I still get 'None' & 'None', and when I try to run a workflow, I get the following error:

---

OSError Traceback (most recent call last)
in ()
----> 1 pp.run()

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py in run(self, plugin, plugin_args, updatehash)
600 if str2bool(self.config['execution']['create_report']):
601 self._write_report_info(self.base_dir, self.name, execgraph)
--> 602 runner.run(execgraph, updatehash=updatehash, config=self.config)
603 datestr = datetime.utcnow().strftime('%Y%m%dT%H%M%S')
604 if str2bool(self.config['execution']['write_provenance']):

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py in run(self, graph, config, updatehash)
42 if self._status_callback:
43 self._status_callback(node, 'start')
---> 44 node.run(updatehash=updatehash)
45 if self._status_callback:
46 self._status_callback(node, 'end')

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py in run(self, updatehash)
485
486 try:
--> 487 result = self._run_interface(execute=True)
488 except Exception:
489 logger.warning('[Node] Error on "%s" (%s)', self.fullname, outdir)

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py in _run_interface(self, execute, updatehash)
569 self._update_hash()
570 return self._load_results()
--> 571 return self._run_command(execute)
572
573 def _load_results(self):

~/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py in _run_command(self, execute, copyfiles)
648 logger.info(message)
649 try:
--> 650 result = self._interface.run(cwd=outdir)
651 except Exception as msg:
652 result.runtime.stderr = '%s\n\n%s'.format(

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py in run(self, cwd, **inputs)
513
514 try:
--> 515 runtime = self._run_interface(runtime)
516 outputs = self.aggregate_outputs(runtime)
517 except Exception as e:

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/spm/base.py in _run_interface(self, runtime)
357 self.mlab.inputs.script = self._make_matlab_command(
358 deepcopy(self._parse_inputs()))
--> 359 results = self.mlab.run()
360 runtime.returncode = results.runtime.returncode
361 if self.mlab.inputs.uses_mcr:

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py in run(self, cwd, **inputs)
513
514 try:
--> 515 runtime = self._run_interface(runtime)
516 outputs = self.aggregate_outputs(runtime)
517 except Exception as e:

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/matlab.py in _run_interface(self, runtime)
160 def _run_interface(self, runtime):
161 self.terminal_output = 'allatonce'
--> 162 runtime = super(MatlabCommand, self)._run_interface(runtime)
163 try:
164 # Matlab can leave the terminal in a barbbled state

~/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py in _run_interface(self, runtime, correct_return_codes)
1011 'No command "%s" found on host %s. Please check that the '
1012 'corresponding package is installed.' % (executable_name,
-> 1013 runtime.hostname))
1014
1015 runtime.command_path = cmd_path

OSError: No command "matlab" found on host Juyoungs-MacBook-Pro.local. Please check that the corresponding package is installed.

[djarecka]

@jykim24 - if you copied-pasted the exact code, there is a typo. matlab_cmd should be an argument to set_mlab_paths, so try spm.SPMCommand.set_mlab_paths(paths='/Applications/MATLAB_R2016b.app/toolbox/spm12/', matlab_cmd='/Applications/MATLAB_R2016b -nodesktop -nosplash')

[jykim24]

@djarecka

Okay, I've tried the the code as below, but this still gives me 'none' as output.

spm.SPMCommand.set_mlab_paths(paths='/Applications/MATLAB_R2016b.app/toolbox/spm12/', matlab_cmd='/Applications/MATLAB_R2016b -nodesktop -nosplash')
print(spm.Info.name())

[satra]

@jykim24 - it seems you are on os x. your matlab command is likely to be:

/Applications/MATLAB_R2016b.app/bin/matlab -nodesktop -nosplash

[djarecka]

thanks @satra, it was my mistake that I wrote that this should be path to matlab.

[jykim24]

@satra @djarecka
Thanks, but even when I change matlab_cmd as you suggested, spm.Info.name() still gives me 'none'.

[satra]

@jykim24 - can you open a terminal and type:

which matlab

if that returns empty, then type:

find /Applications/MATLAB_R2016b -name "matlab"

let's first make sure we can find matlab via the terminal.

[jykim24]

@satra
'which matlab' returns nothing, and the second line returns 'No such file or directory'.