Spm.utils applytransform mat file description

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1

Hi ,

Can someone tell me the description of each element in the matrix of input mat file for spm.utils applytransform

mat: (an existing file name)
file holding transform to apply

Its a 4*4 matrix , but nowhere I can find which element in the matrix corresponds to pitch,roll,yaw, xyz translation, scaling, affine .

2

Hi Sandeep,

Have a look at spm_matrix.m: given a parametrisation of an affine transformation, it will return the corresponding 4x4 transformation matrix. This is the function called if you enter “Reorientation Parameters” instead of “Reorientation Matrix”.

Best,
Guillaume.

3

thanks for the reply.

4

Hi ,

So I am using spm12 standalone and MCR, is it possible to call spm_matrix.m in nipype with this setup, it looks like there is no way to do that from my research online so far. Can you help me with a small script on how to do that.

5

Hi Sandeed,

it would be useful if you could provide more details about what you are trying to do as there might be several ways to achieve the same goal.

I don’t know how this would integrate with nipype but if you create a text file called transform.m containing:

mat = load(inputs{1});
spm_imatrix(mat.M)

you can use it with the Standalone SPM12 to load an affine transformation matrix from file and display its parametrisation:

spm12-matlab script transform.m reorient.mat

All the best,
Guillaume.

6

The spm functions do well with full version of matlab and nipype setup , but I can find a way to implement the spm functions with MCR and nipype setup.

So I currently am implementing VBM (basic steps: reorientation, segmentation, normalization, smoothing) on some structural t1w niftis and I am using nipype , MCR and spm12 standalone to achieve this. So my spm12 standalone uses Matlab common runtime in nipype.
from nipype.interfaces import spm
spm.SPMCommand.set_mlab_paths(
matlab_cmd=’/opt/spm12/run_spm12.sh /opt/mcr/v95 script’, use_mcr=True)
spm.SPMCommand().version

returns ‘12.7507’
and I am able to run my vbm pipeline fully just fine.

I currently pass reorientaion parameters like (x,y,z,pitch roll,yaw) in a .mat file as that is the only option which is given by the function nipype.interfaces.spm.utils.applytransform()

The goal is: I want to be able to pass reorientation parameters as arguments without needing a .mat file as input. The applytransform() does not allow that, so I am trying to implement the spm_imatrix() function as you said, but its implementation under MCR is not doable as of my knowledge. I know that custom spm functions under a regular matlab work fine, the problem is using MCR .

So if you can help , please let me know how to implement spm_imatrix() with MCR.

7

@Sandeep_Panta - i think we would need a little more info. but in general you can stick anything inside a function node. if you are trying to do this as part of a workflow, i would recommend that.

9

Say I want to implement spm_matrix.m function from spm12 standalone (using MCR) as a function node using nipype. Could you give me a sample script of that since I am not sure how to implement that. Should I expect the foll. script to work:

import nipype.pipeline.engine as pe
from nipype.interfaces.utility import Function
pe.Node(interface=Function(function=spm_matrix),name=‘test_spm’)