Hello, I’m working in nipype with fsl and trying to create a design.fsf file using the functions SpecifyModel() and Level1Design():
modelfit = pe.Workflow(name='modelfit')
modelfit.base_dir = os.path.abspath('./level1design/') #os.path.abspath('./fsl/workingdir')#where the .fsf and other output will be saved
modelfit.config = {
"execution": {
"crashdump_dir": os.path.abspath('./fsl/crashdumps')
}
}
# Use nipype.algorithms.modelgen.SpecifyModel to generate design information
modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec", output_names="session_info")
modelspec.inputs.input_units = 'secs'
modelspec.inputs.functional_runs = func_scan
modelspec.inputs.high_pass_filter_cutoff = 50
modelspec.inputs.time_repetition = 1.962
modelspec.inputs.subject_info = my_subject_info
# Use nipype.interfaces.fsl.Level1Design to generate a run specific fsf file for analysis
level1design = pe.Node(interface=fsl.Level1Design(),name="level1design",input_names='session_info',output_names="fsf_file")
level1design.inputs.interscan_interval = 0 # ask in forum?
level1design.inputs.bases = {'dgamma': {'derivs': True}}
level1design.inputs.model_serial_correlations = bool(False)
modelfit.connect([
(modelspec, level1design, [('session_info', 'session_info')])
])
os.chdir(designpath)#data_path)
mdl = modelfit.run()
However, when I run the above code to create my .fsf file and try to load the file into the feat_gui I get the following error:
bad operation list "": must be one or more of array, read, unset, or write
bad operation list "": must be one or more of array, read, unset, or write
while executing
"trace remove variable fmri(analysis) [ lindex $varcom 0 0] [ lindex $varcom 0 1]"
(procedure "feat5:load" line 24)
invoked from within
"feat5:load .r 1 /Users/haileytrier/Desktop/Prolific_output/13Aug2019_Expt_Data/processed_data/subj001/design0/level1design/modelfit/level1design/run0...."
("eval" body line 1)
invoked from within
"eval "$command $outputfile1" "
(procedure "feat_file:invoke" line 35)
invoked from within
"feat_file:invoke .wdialog1 a a a :: {feat5:load .r 1}"
invoked from within
".wdialog1.f4.but_ok invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .wdialog1.f4.but_ok"
(command bound to event)
My .fsf file uses FEAT version 5.98, and when I load a similar design.fsf file in FEAT version 6.00 it loads without errors. So I think either I need to change the version of FEAT that nipype produces, or there is some other issue with my .fsf file that the above error is referencing. I’d appreciate any advice, thanks.