SPM's NewSegment can't find TPM file

[juan-d]

Hello,

I'm following the Nipype preprocessing tutorial at workshop/nipype_tutorial/notebooks/handson_preprocessing.ipynb.

When I get to creating the node for NewSegment I am getting an error. These are the relevant lines of code:

# Specify which SPM to use
from nipype.interfaces.matlab import MatlabCommand
MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')

from nipype.interfaces.spm import NewSegment

# Use the following tissue specification to get a GM and WM probability map
tpm_img ='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'
tissue1 = ((tpm_img, 1), 1, (True,False), (False, False))
tissue2 = ((tpm_img, 2), 1, (True,False), (False, False))
tissue3 = ((tpm_img, 3), 2, (True,False), (False, False))
tissue4 = ((tpm_img, 4), 3, (False,False), (False, False))
tissue5 = ((tpm_img, 5), 4, (False,False), (False, False))
tissue6 = ((tpm_img, 6), 2, (False,False), (False, False))
tissues = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6]

segment = Node(NewSegment(tissues=tissues), name='segment')

I have tried to run the commands above as they are and also replacing the SPM version in Neurodesk (r7771). I also tried loading spm prior to running them:

import module
await module.load('spm12/r7771')

In all cases, I am getting the following error message:

TraitError: Each element of the 'tissues' trait of a NewSegmentInputSpec instance must be a tuple of the form: (a tuple of the form: (a pathlike object or string representing an existing file, an integer), an integer, a tuple of the form: (a boolean, a boolean), a tuple of the form: (a boolean, a boolean)), but a value of (('opt/spm12-r7771/spm12_mcr/spm12/tpm/TPM.nii', 1), 1, (True, False), (False, False)) <class 'tuple'> was specified.

The folder /opt/spm12-r7219/spm12_mcr/spm12 does not exist (when I search it with !ls)

I also tried the following as in a recent thread #725

!pip install spm12
import module
await module.load('spm12')

I got the same error.

Thank very much you for your help with the above.

[stebo85]

I have a look

[stebo85]

Dear @juan-d - found the problem. The tutorial you are following has a hardcoded path that's incorrect.

This works:

import module
await module.load('spm12/r7771')

from nipype.interfaces.matlab import MatlabCommand
from nipype.interfaces.spm import NewSegment
import shutil
from pathlib import Path
import nipype.interfaces.spm as spm
from nipype import Node, Workflow

container_dir = Path(shutil.which("spm12")).parent
container_name = container_dir.name
tpm_img = container_dir / f"{container_name}.simg" / "opt/spm12/spm12_mcr/spm12/spm12/tpm/TPM.nii"

# Use the following tissue specification to get a GM and WM probability map
tissue1 = ((tpm_img, 1), 1, (True,False), (False, False))
tissue2 = ((tpm_img, 2), 1, (True,False), (False, False))
tissue3 = ((tpm_img, 3), 2, (True,False), (False, False))
tissue4 = ((tpm_img, 4), 3, (False,False), (False, False))
tissue5 = ((tpm_img, 5), 4, (False,False), (False, False))
tissue6 = ((tpm_img, 6), 2, (False,False), (False, False))
tissues = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6]

segment = Node(NewSegment(tissues=tissues), name='segment')

[juan-d]

Dear @stebo85.

Thanks a lot for that. That worked!

I bumped into a similar problem further down in the tutorial when running FSL's FLIRT BBR. The issue this time was finding bbr.sch (the BBR scheme file). I used the same approach as in your solution and I was able to successfully provide the path. I share it here in case others bump into this issue:

import module
await module.load('fsl/6.0.7.18')

container_dir = Path(shutil.which("fsl")).parent
container_name = container_dir.name
tpm_schedule = container_dir / f"{container_name}.simg" / "opt/fsl-6.0.7.18/src/fsl-flirt/flirtsch/bbr.sch"

BTW, to find the exact path (which was different from the one in the turorial), I launched an instance of Neurodesktop (virtual desktop), loaded fsl/6.0.7.18, which prints the path to the container as it loads, and then ran a find command within the container for the bbr.sch file.

[stebo85]

That's great - thank you ! We will add this to our examples :)