Closed nbeliy closed 6 months ago
I am not sure what you are asking to do? it does tell the user how to set it up, are you asking a new feature? which would not be a bug --- if ubuntu virtual under window, it a dcm2niix issue (it cannot work)
I'm not sure if I would call this a bug as it seems to be working as intended, if you execute dcm2niix
from the same location as your executing dcm2niix4pet
what is the output?
The feature is primarily intended to help windows users who aren't able to put dcm2niix onto their path for various reasons, e.g. they don't have admin access on their work machines. See the instructions under the windows only section of installation here -> https://pet2bids.readthedocs.io/en/latest/installation.html#python
We always check to see if dcm2niix is installed as we are unable to convert from dicom without it. On a posix machine we check the path with check_posix then if it's not found there we check the config file to see if the dcm2niix
binary is specified in the config here.
I'm confident that if you either add dcm2niix
to your PATH
variable or run --set-dcm2niix-path
with the full file path to your binary you should be able to resolve the error you encountered.
Maybe I was unclear.
pet2bids
runs as intended if I setup path with --set-dcm2niix-path
. But it still show an error that dcm2niix
not installed.
I would like that you change the check for installed dcm2niix
to consider the path setup with --set-dcm2niix-path
.
It is absolutely not critical issue, more just annoying, printing a fake error.
Updated per request.
Describe the bug If
dcm2niix
is installed not in the user's path, but setup using--set-dcm2niix-path
option,dcm2niix4pet
produce error aboutdcm2niix
not being installed. Outside the shown error, the conversion behave normally.To Reproduce
This is caused by
check_posix
, who do not attempt to retrieve path todcm2niix
, unlikecheck_for_dcm2niix
just belowExpected behaviour No error shown.
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