"rapidtide2 is a rapidtide script, but is not installed" after Docker installation
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Hi everybody
After following the guide for installing rapidtide (docker installation), when I try to run rapidtide2 through the docker I receive the message "rapidtide2 is a rapidtide script, but is not installed". I'm not very practical of using docker. Did I miss something? I installed the latest version with the tag :latest. I'm using Ubuntu 18.04.4 LTS
Thank you
The "latest" container follows the development branch (currently 2.0alpha26), and it uses a slightly different calling syntax. Try your command again, but replace "rapidtide2" with "rapidtide2x_legacy", which uses the old calling syntax. Alternatively, when you download the docker container, you could specify "1.9.4" instead of "latest".
Let me know if that works.
The "latest" container follows the development branch (currently 2.0alpha26), and it uses a slightly different calling syntax. Try your command again, but replace "rapidtide2" with "rapidtide2x_legacy", which uses the old calling syntax. Alternatively, when you download the docker container, you could specify "1.9.4" instead of "latest".
Let me know if that works.
Hi, thank you very much for answering. If I try to download versions 1.9.4, 1.9.3 or 1.9.2 I get the message
"Error response from daemon: manifest for fredericklab/rapidtide:1.9.4 not found: manifest unknown: manifest unknown"
While with 1.9.0 or 1.9.1 it works properly. Any hint on that?
Anyway, with version 1.9.1 my command runs correctly, so thank you for solving the first issue. Please let me know if you have any clue on why I couldn't download version 1.9.4
Ok, I did a deep dive and found three major issues, each of which just go to show I'm terrible at managing version numbers. First off, as of version 1.9.2 or so I was using the wrong version tag "v1.9.2", "v1.9.3", "v1.9.4", instead of the version without the "v". This caused an internal error in the Docker container when trying to find binaries, which led to your issue. I've fixed all of this, and released it as 1.9.5. So fredericklab/rapidtide:1.9.5 should get you what you want. Sorry!
Hi @bbfrederick , thank you for fixing this!
Now, I'm able to run v1.9.5 properly, but I'm getting an error after the "Time lag estimation pass 2".
The command was
rapidtide2 /data_in/$in_ds /data_out/$out_ds -N 0 -r -10,60 -F 0.0,0.2 --lagmaxthresh=40 --ampthresh=0.2 --includemask=/mask_in/$mask --noglm --nofitfilt --regressor=/reg_in/$text_file_reg --regressorfreq=100
The last lines printed on stdin are
Time lag estimation pass 2
Percent complete: [ ]
...
Percent complete: [############################################################] 100.000%
Correlation fitted in 230918 voxels
ampfails= 0
lagfails= 0
widthfail= 0
edgefail= 0
fitfail= 0
Garbage collector: collected 0 objects.
rereading /data_in/***.nii for GLM filter, please wait
done
Traceback (most recent call last):
File "/usr/local/miniconda/bin/rapidtide2", line 4, in
import('pkg_resources').run_script('rapidtide==0+unknown', 'rapidtide2')
File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 651, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/miniconda/lib/python3.7/site-packages/pkg_resources/init.py", line 1448, in run_script
exec(code, namespace, namespace)
File "/usr/local/miniconda/lib/python3.7/site-packages/rapidtide-0+unknown-py3.7.egg/EGG-INFO/scripts/rapidtide2", line 3348, in
main()
File "/usr/local/miniconda/lib/python3.7/site-packages/rapidtide-0+unknown-py3.7.egg/EGG-INFO/scripts/rapidtide2", line 3339, in main
")",
TypeError: sequence item 4: expected str instance, NoneType found
Any guess?
This is a nightmare. I'm not sure exactly why this is so hard to fix - I think it's some weird combination of Docker, git, and versioneer not wanting to play well together. That said, I THINK things are fixed now in 1.9.6. Let me know if that's true...
Thank you, version 1.9.6 is working! Great job!