Nipype: fsl Level1Design Traiterror

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1

Hi there,

I’ve been trying to run a level one design using nipype and the fsl interfaces. As can be seen below, i get a
trait error (TraitError: The trait ‘ev_files’ of a Level1DesignOutputSpec instance is an existing file name, but the path REMOVED does not exist ). This of course makes it impossible to create the event files , fsf files, or the mat files. The other triait errors I have seen on here with this error seem to have to do with docker. I don’t have a writing error as far as I can tell and memory is not an issue with the computer.

I would greatly appreciate any tips on how to solve this or how others have gone about resolving trait errors like this where a file that should have been generated is not found.

Thank you!
Marlen

Here is the printout of the crash file with redacted information for ease of readability.

Node: LEVELONE.modelprep.level1design
Working directory: /var/folders/48/_q3xrnms1sqbtkhrvrj52x400000gp/T/tmpxajxgq9q/LEVELONE/modelprep/_ROI_id_R_DLPFC_BLOCK_TMS_subject_id_P101/level1design

Node inputs:

bases = {‘dgamma’: {‘derivs’: False}}
contrasts = [(‘OFF’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block1’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block2’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block3’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block4’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block5’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0]), (‘Block6’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0]), (‘Block7’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0]), (‘Block8’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0]), (‘Block9’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0]), (‘Block10’, ‘T’, [‘OFF’, ‘B1’, ‘B2’, ‘B3’, ‘B4’, ‘B5’, ‘B6’, ‘B7’, ‘B8’, ‘B9’, ‘B10’], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0])]
ignore_exception = False
interscan_interval = 2.5
model_serial_correlations = True
orthogonalization =
session_info = [{‘cond’: [{‘duration’: [17.5], ‘name’: ‘B1’, ‘onset’: [32.399999999999999]}], ‘hpf’: 100.0, ‘regress’: [{‘name’: ‘Realign1’, ‘val’: [REMOVED]}, {‘name’: ‘Realign2’, ‘val’: [REMOVED]}, {‘name’: ‘Realign3’, ‘val’: [REMOVED]}, {‘name’: ‘Realign4’, ‘val’: [REMOVED]}, {‘name’: ‘Realign5’, ‘val’: [REMOVED]}, {‘name’: ‘Realign6’, ‘val’: [REMOVED]}, {‘name’: ‘Outlier1’, ‘val’: [REMOVED]}], ‘scans’: ‘/var/folders/48/_q3xrnms1sqbtkhrvrj52x400000gp/T/tmpzpv73ay0/LEVELONE/modelprep/_ROI_id_R_DLPFC_BLOCK_TMS_subject_id_P101/modelspec/Func_Ready_mcf_st_flirt_smooth.nii.gz’}]

Traceback:
Traceback (most recent call last):
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py”, line 44, in run
node.run(updatehash=updatehash)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 487, in run
result = self._run_interface(execute=True)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 571, in _run_interface
return self._run_command(execute)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 668, in _run_command
_save_resultfile(result, outdir, self.name)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/utils.py”, line 244, in save_resultfile
result.outputs.set(**modify_paths(outputs, relative=True, basedir=cwd))
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/util/deprecated.py”, line 32, in wrapper
return fn(*args, **kw)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/has_traits.py”, line 1551, in set
trait_change_notify=trait_change_notify, **traits)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/has_traits.py”, line 1543, in trait_set
setattr( self, name, value )
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 341, in validate
value = super(MultiPath, self).validate(object, name, newvalue)
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_types.py”, line 2336, in validate
return TraitListObject( self, object, name, value )
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2313, in init
raise excp
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2305, in init
value = [ validate( object, name, val ) for val in value ]
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2305, in
value = [ validate( object, name, val ) for val in value ]
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_types.py”, line 2336, in validate
return TraitListObject( self, object, name, value )
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2313, in init
raise excp
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2305, in init
value = [ validate( object, name, val ) for val in value ]
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2305, in
value = [ validate( object, name, val ) for val in value ]
File “/Users/marlengonzalez/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 112, in validate
self.info_text, value))
traits.trait_errors.TraitError: The trait ‘ev_files’ of a Level1DesignOutputSpec instance is an existing file name, but the path ‘/private/var/folders/48/_q3xrnms1sqbtkhrvrj52x400000gp/T/tmpxajxgq9q/LEVELONE/modelprep/_ROI_id_R_DLPFC_BLOCK_TMS_subject_id_P101/level1design/ev_B1_0_1.txt’ does not exist.

2

I didn’t get if you run this specific example in a docker container. If yes, did you run other, simpler, workflows in the same container?

did you specify base_dir of your Workflow?

3

Hi @djarecka! Thanks for the reply. Although I’be seen this type of error around Neurostars relating to use of virtual machines, my own problem is actually with my own computer running everything. I checked to make sure that there are no base_dir issues and indeed everything matches up. I also tried to play around with how I call up the event files using the function below but that doesn’t seem to help.

Any further help would be appreciated!

Marlen

def subjectinfo(subject_id):
import pandas as pd
from nipype.interfaces.base import Bunch
from os.path import join as opj
#EV_FILE= opj(‘preproc’,‘TMS_Block_Timings.txt’)
trialinfo = pd.read_table(’~/Documents/Projects/spTMS-fMRI/fMRI_data/PREPROC_Try2/preproc/TMS_Block_Timings.txt’)
trialinfo.head()
conditions = []
onsets = []
durations = []
for group in trialinfo.groupby(‘Event’):
conditions.append(group[0])
onsets.append(group[1].Onset.tolist())
durations.append(group[1].Duration.tolist())
subject_info = [Bunch(conditions=conditions,
onsets=onsets,durations=durations,
#amplitudes=None,
#tmod=None,
#pmod=None,
#regressor_names=None,
#regressors=None
)]
return subject_info # this output will later be returned to infosource
# Function node to use getsubjectinfo
getsubjectinfo = Node(Function(input_names=[‘subject_id’],
output_names=[‘subject_info’],
function=subjectinfo),
name=‘getsubjectinfo’)

4

I don’t see Workflow in this code. Do you use nipype Workflow or only Node?

If you use Workflow can you please paste the code showing how you define and use it.

5

Hi @djarecka,

You were totally right. I have two workflows connected into a larger workflow. Once I specified the base_dir, in the larger workflow this error went away. Thanks!

LEVELONE = Workflow(name=‘LEVELONE’)
LEVELONE.base_dir= preproc_dir

6

great!
base_dir is important when using Workflow! We probably should think about better warnings.