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Freesurfer installation overwrites the PATH environmental variable #449

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ellisdg opened this issue May 3, 2022 · 1 comment · Fixed by #462
Closed

Freesurfer installation overwrites the PATH environmental variable #449

ellisdg opened this issue May 3, 2022 · 1 comment · Fixed by #462

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@ellisdg
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ellisdg commented May 3, 2022

After creating a docker image, I noticed that the directory locations for any package installed before Freesurfer were not listed in the PATH environmental variable.

Looking at the template for FreeSurfer, it looks like it completely overwrites the PATH variable instead of simply prepending the Freesurfer directory locations like FSL does. Is there a reason for this?
pwighton added a commit to pwighton/neurodocker that referenced this issue Aug 3, 2022
@pwighton
[FIX] fix for issue ReproNim#449
2625184
@pwighton pwighton mentioned this issue Aug 3, 2022
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@pwighton
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pwighton commented Aug 3, 2022

Hi @ellisdg, thanks for pointing this out. I just submitted a PR (#462) that should fix this issue.

kaczmarj pushed a commit that referenced this issue Aug 4, 2022
@pwighton
[FIX] fix for issue #449 (#462)
97b7a3c
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Fix for issue #449 pwighton/neurodocker
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@pwighton @ellisdg