phantomas
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ecaruyer
Create realistic digital phantoms in diffusion MRI.
After downloading and installing phantomas, I get the following when I run "phantomas_dwis -h" Traceback (most recent call last): File "/usr/local/bin/phantomas_dwis", line 19, in from phantomas.mr_simul.fod \ File "/media/hda6/Experimenten/phantomas/phantomas/mr_simul/fod.py", line...
On the left is the old version of the tracking mask for the the isbi phantom and on the right the new one (made using the phantomas_rois scripts, this is...
I think Samuel St-Jean has had this issue in the past. It seems that for some configuration of python environment running the phantomas_dwi generates "empty" diffusion-weighted images. The geometry and...
Create mask of white matter, as well as a mask for each bundle.
Seems like white matter attenuation (as well as diffusion-weighted images) have negative values. Thanks @samuelstjean for letting me know!
The translation part of the affine matrix seems wrong, or at least does not place the center of the volume to position (0, 0, 0). (Thanks @jchoude for letting me...