caisr / qsm Goto Github PK

Hello,

I was wondering wheather I can use the SWI magnitude and phase images as input for the QSM reconstruction instead of the gradient echo data (GRE). I have done it and I was able to obtain the QSM final map. Do you know if I can rely on those results?

Thank you so much,

Marina.

Hi,

I have tried running the QSM reconstruction using the --single_pass option. I would like to know what is the exact difference If I use this option or not. From what I understand, if I use the single pass option it runs a single QSM reconstruction per echo instead of two, so for the reconstruction it uses a mask produced by thresholding and binarising the magnitude signal, but it is skipping the second reconstruction which applies morphological operations. Is that correct?

Thank you so much,

Marina.

Hi, I was wondering if the qsm pipleine can deal with multiecho data? I have tried to use the QSMxT for multiecho data but then I also need the T1w and T2*w right?

I wonder what are -in a nutshell- the similarities/differences between this pipeline and the QSMxT one? Is one an evolution of the other and therefore recommended to be used generally or simply tackle different goals/use-cases?

thanks!

Hi I just tried the docker tool on my mac on the test data provided with the python code and got the following output:

root@8bd479b57fd0:/data# tgv_qsm -p epi3d_test_phase.nii.gz -m epi3d_test_mask.nii.gz -f 2.89 -t 0.027 -o epi3d_test_QSM

TGV-QSM <<<<<

loading files...
phase: epi3d_test_phase.nii.gz
mask: epi3d_test_mask.nii.gz
output: epi3d_test_phaseepi3d_test_QSM_{number:03d}.nii.gz
Resampling phase data...
/usr/lib/python2.7/dist-packages/scipy/ndimage/interpolation.py:430: UserWarning: The behaviour of affine_transform with a one-dimensional array supplied for the matrix parameter has changed in scipy 0.18.0.
"The behaviour of affine_transform with a one-dimensional "
Resampling magnitude/mask data...
Data looks good!
Processing initial laplacian of epi3d_test_phase.nii.gz ...
Processing QSM epi3d_test_phase.nii.gz ...
Factor 1.0 (1 of 1) - alpha = (0.0015, 0.0005)
Iterations: 1000 (1 of 1)
Progress: [ ] 0.0% Illegal instruction
root@8bd479b57fd0:/data#

Do yo have any insights on what could be wrong?

Thank you again for sharing this useful tool!