MRTrix2TrackVis : error importing 'affine_from_fsl_mat_file' from 'dipy.tracking.utils'

[hollysully]

I am trying to use MRTrix2TrackVis (https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.mrtrix.convert.html)

When I run the lines of code below, I get this error when I run the last line: ImportError: cannot import name 'affine_from_fsl_mat_file' from 'dipy.tracking.utils' (/opt/anaconda3/lib/python3.11/site-packages/dipy/tracking/utils.py)

import nipype.interfaces.mrtrix as mrt
tck2trk = mrt.MRTrix2TrackVis()
tck2trk.inputs.in_file = 'dwi_CSD_tracked.tck'
tck2trk.inputs.image_file = 'diffusion.nii'
tck2trk.run()    

The error seems to relate to what is discussed on this page (nipy/nipype#3413), but I am not sure how to proceed

[skoudoro]

Hi @hollysully,

It has been a long time that this function has been removed from DIPY codebase. see #1939

I recommend you to ask the creator of this Nipype function to update the code directly in Nipype. I agree that it is related to nipy/nipype#3413.

I hope it helps.

[hollysully]

Thank you! Could you recommend another method for extracting FA from an MRtrix .tck tract? Maybe a tutorial?

[arokem]

How about this? https://docs.dipy.org/stable/examples_built/streamline_analysis/afq_tract_profiles.html#sphx-glr-examples-built-streamline-analysis-afq-tract-profiles-py

[hollysully]

Thank you, Ariel! Do you also have a suggestion for segmenting the tract?

[skoudoro]

How about this command line: https://docs.dipy.org/stable/interfaces/bundle_segmentation_flow.html

[skoudoro]

this one can be helpful also: https://docs.dipy.org/stable/interfaces/buan_flow.html

[Garyfallidis]

The command line dipy_convert_tractogram was created to do such things @hollysully. Meaning convert tractograms. Then you can simply use an FA or any other image independently. They do not need to be in the same file.