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I am trying to perform FLIRT registration vi nipype package in Google Colab, but I don't know how to fix it. If someone knows how to fix it, please help me.

!pip install nipype
from nipype.interfaces import fsl
from nipype.testing import example_data
flt = fsl.FLIRT(bins=640, cost_func='mutualinfo')
flt.inputs.in_file = '/content/MaskP1.nii.gz'
flt.inputs.reference = '/content/P1_FL_fim.nii.gz'
flt.inputs.output_type = "NIFTI_GZ"
res = flt.run()

The error message is: OSError: No command "flirt" found on host 34bc2567880d. Please check that the corresponding package is installed.

Isabella
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1 Answers1

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I guess the issue is that there is no FSL installed on the machine in Google Colab. If you try to type on a cell something like !echo ${FSLDIR} does it work?

alegiac
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