Windows installing without docker

[desserdmi]

Summary

Platform details:

Choose one:

• [ ] Local environment

Windows 7

• [ ] Container

• Heudiconv version:

0.5.4

Hi guys,

heudiconv runs perfectly on Linux and MAC for me using docker. I have tried to install heudiconv with using pip and conda. It seems to have problems with dependencies. I think the conflict is mainly due to dcm2niix dependencies. Using Python 2.7. it is possible to install and to run heudiconv, but while executing the conversion “[Error 32] File is being used by another process” appears (command: heudiconv -d dicom/{subject}/{session}//DICOM/.dcm -o bids -s 01 -ss 01 -f script/heuristic.py)

I have already posted this issue on neurostars:

https://neurostars.org/t/dicom-to-bids-conversion-on-windows/5009/6

Do you have any ideas how to fix it?

(I only have Windows 7 in my lab available at this moment)

Any help would be appreciated!

Best,

Dima

[mgxd]

Hi Dima,

We don't explicitly test heudiconv on Windows - our preferred method is via Docker container. Your best bet is to try installing the docker toolbox for legacy systems https://docs.docker.com/toolbox/toolbox_install_windows/

I'll see if I can submit a patch that hopefully fixes the error you posted.

[mgxd]

@desserdmi

I've created a patch, you can install with

pip install https://github.com/mgxd/heudiconv/archive/fix/win.zip

can you retry your conversion with this version?

[desserdmi]

Hi,

thank you for your reply!

I have installed the patch. Now, the problem ist an old nibabel version. dcm2niix requires nibabel 2.1.2. The batch installed 2.0.2 which is a dependency of any other package of heudiconv.

At the end I get the error message: DCM2niix failed to run. "TypeError: environment can only contain strings"

Best,

Dima

Am Mi., 18. Sept. 2019 um 17:52 Uhr schrieb Mathias Goncalves < [email protected]>:

@desserdmi https://github.com/desserdmi

I've created a patch, you can install with

pip install https://github.com/mgxd/heudiconv/archive/fix/win.zip

can you retry your conversion with this version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nipy/heudiconv/issues/371?email_source=notifications&email_token=AI5WV575EHCDJIZADPXTSMLQKJFCJA5CNFSM4IYAJMYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AROQA#issuecomment-532748096, or mute the thread https://github.com/notifications/unsubscribe-auth/AI5WV56C3C4FJMR3KZM7E5LQKJFCJANCNFSM4IYAJMYA .

[desserdmi]

P.S. on another virtualenv I get the Error: https://stackoverflow.com/questions/10842428/can-select-be-used-with-files-in-python-under-windows

So I think there is a select() funktion anywhere in the script and windows i not able to deal with it :))

Cheers,

Dima

Am Mi., 18. Sept. 2019 um 19:40 Uhr schrieb Dmitriy Desser < [email protected]>:

Hi,

thank you for your reply!

I have installed the patch. Now, the problem ist an old nibabel version. dcm2niix requires nibabel 2.1.2. The batch installed 2.0.2 which is a dependency of any other package of heudiconv.

At the end I get the error message: DCM2niix failed to run. "TypeError: environment can only contain strings"

Best,

Dima

Am Mi., 18. Sept. 2019 um 17:52 Uhr schrieb Mathias Goncalves < [email protected]>:

@desserdmi https://github.com/desserdmi

I've created a patch, you can install with

pip install https://github.com/mgxd/heudiconv/archive/fix/win.zip

can you retry your conversion with this version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nipy/heudiconv/issues/371?email_source=notifications&email_token=AI5WV575EHCDJIZADPXTSMLQKJFCJA5CNFSM4IYAJMYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AROQA#issuecomment-532748096, or mute the thread https://github.com/notifications/unsubscribe-auth/AI5WV56C3C4FJMR3KZM7E5LQKJFCJANCNFSM4IYAJMYA .

[desserdmi]

P.P.S.

Sorry for spamming and bothering you with that. My main problem with docker toolbox is actually to run it behind the proxy of the lab.. It is much more complicated as with normal docker distribution :/

What do you actually think about developing some kind of compiled version with GUI for heudiconv using QT?

I mean I could try it on my own (I am currently MD student) but any supervision/support would be very nice…

Best,

Dima

Am Mi., 18. Sept. 2019 um 19:48 Uhr schrieb Dmitriy Desser < [email protected]>:

P.S. on another virtualenv I get the Error: https://stackoverflow.com/questions/10842428/can-select-be-used-with-files-in-python-under-windows

So I think there is a select() funktion anywhere in the script and windows i not able to deal with it :))

Cheers,

Dima

Am Mi., 18. Sept. 2019 um 19:40 Uhr schrieb Dmitriy Desser < [email protected]>:

Hi,

thank you for your reply!

I have installed the patch. Now, the problem ist an old nibabel version. dcm2niix requires nibabel 2.1.2. The batch installed 2.0.2 which is a dependency of any other package of heudiconv.

At the end I get the error message: DCM2niix failed to run. "TypeError: environment can only contain strings"

Best,

Dima

Am Mi., 18. Sept. 2019 um 17:52 Uhr schrieb Mathias Goncalves < [email protected]>:

@desserdmi https://github.com/desserdmi

I've created a patch, you can install with

pip install https://github.com/mgxd/heudiconv/archive/fix/win.zip

can you retry your conversion with this version?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nipy/heudiconv/issues/371?email_source=notifications&email_token=AI5WV575EHCDJIZADPXTSMLQKJFCJA5CNFSM4IYAJMYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AROQA#issuecomment-532748096, or mute the thread https://github.com/notifications/unsubscribe-auth/AI5WV56C3C4FJMR3KZM7E5LQKJFCJANCNFSM4IYAJMYA .