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bids-apps / oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI
Apache License 2.0
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Cannot find module yargs #13

Open LJWilliams opened 7 years ago

LJWilliams commented 7 years ago

I just installed oppni from the docker image and I cannot get it to run. The file has already run with several other apps that require bids format.

Suggestions would be greatly appreciated.

docker run --rm -v /Users/lwilliams/Documents/Studies/Test:/data:ro -v /Users/lwilliams/Documents/Studies/Test/derivatives/oppni:/out default/oppni /data /out participant --participant_label sub-01

Traceback (most recent call last): File "/oppni/oppni.py", line 222, in run_oppni() File "/oppni/oppni.py", line 185, in run_oppni validate_bids_spec(args.bids_dir) File "/oppni/oppni.py", line 78, in validate_bids_spec run_cmd(cmd) File "/oppni/oppni.py", line 67, in run_cmd raise Exception("Non zero return code: %d"%process.returncode) Exception: Non zero return code: 1 module.js:471 throw err; ^

Error: Cannot find module 'yargs' at Function.Module._resolveFilename (module.js:469:15) at Function.Module._load (module.js:417:25) at Module.require (module.js:497:17) at require (internal/module.js:20:19) at Object. (/usr/lib/node_modules/bids-validator/bin/bids-validator:25:5) at Module._compile (module.js:570:32) at Object.Module._extensions..js (module.js:579:10) at Module.load (module.js:487:32) at tryModuleLoad (module.js:446:12) at Function.Module._load (module.js:438:3)

raamana commented 7 years ago

Hey Lynne, the issue seems to be with validating BIDS specification, done via a javascript ouside OPPNI.

Do you by chance have the BIDS validator installed? If not could try installing this: https://www.npmjs.com/package/bids-validator

LJWilliams commented 7 years ago

Hi,

Thanks for the quick response. I have run other BIDS apps on the dataset, so I thought that it would run this time. I will try the validator again and let you know if it doesn't work.

Thank-you, Lynne

On 1 June 2017 at 10:28, Pradeep Reddy Raamana notifications@github.com wrote:

Hey Lynne, the issue seems to be with validating BIDS specification, done via a javascript ouside OPPNI.

Do you by chance have the BIDS validator installed? If not could try installing this: https://www.npmjs.com/package/bids-validator

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/oppni/issues/13#issuecomment-305563437, or mute the thread https://github.com/notifications/unsubscribe-auth/ACSMCwaw_nCix9f1AwDuFiAKdEEyPbl3ks5r_vSogaJpZM4NtRoq .

raamana commented 7 years ago

Actually, @chrisfilo has a better idea to make the installation of BIDS validator, part of OPPNI itself. This additional feature is being tested, and will update you in a bit.

LJWilliams commented 7 years ago

Hello,

My dataset comes back being a valid dataset with both the online and command-line versions of the validator (no errors and no warnings). I still get the same error when trying to run oppni from the docker container.

Lynne

Summary: Available Tasks: Available Modalities: 8713 Files, 972.57MB semantic decision (ADDT) T1w 1 - Subject T2w 1 - Session bold

On 1 June 2017 at 10:28, Pradeep Reddy Raamana notifications@github.com wrote:

Hey Lynne, the issue seems to be with validating BIDS specification, done via a javascript ouside OPPNI.

Do you by chance have the BIDS validator installed? If not could try installing this: https://www.npmjs.com/package/bids-validator

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/oppni/issues/13#issuecomment-305563437, or mute the thread https://github.com/notifications/unsubscribe-auth/ACSMCwaw_nCix9f1AwDuFiAKdEEyPbl3ks5r_vSogaJpZM4NtRoq .

LJWilliams commented 7 years ago

Thank-you

On Jun 1, 2017, at 11:06, Pradeep Reddy Raamana notifications@github.com wrote:

Actually, @chrisfilo has a better idea to make the installation of BIDS validator, part of OPPNI itself. This additional feature is being tested, and will update you in a bit.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

LJWilliams commented 7 years ago

Thank-you. I reinstalled OPPNI with the BIDS validator and it gets me through that. However, the Matlab Runtime is saying that it isn't finding a function. Would you like me to start a new issue?

Lynne

docker run --rm -v /Users/lwilliams/Documents/Studies/Test:/data:ro -v /Users/lwilliams/Documents/Studies/Test/derivatives/oppni:/out oppni/oppni /data /out participant --participant_label sub-01

This dataset appears to be BIDS compatible. Summary: Available Tasks: Available Modalities: 680 Files, 951.13MB semantic decision (ADDT) T1w 1 - Subject T2w 1 - Session bold

run_oppni.sh /opt/mcr/v80/ /data /out participant --participant sub-01 --run_name linebisection --task_design event

Warning: application is running on a locale different from the original platform locale. WARNING: no contrast is specified. By default, will run all task conditions vs. baseline WARNING: no analysis specified. Using default model selection WARNING: the --ndrop field is empty. The default is setting ndrop=0 (no non-equilibrium scans dropped) WARNING: the --atlasfile field is empty. No spatial normalization is possible Undefined function or variable "tsvfile_list".

Error in bids_parsejobs (line 113)

Error in run_oppni_bids (line 75)

MATLAB:UndefinedFunction

Unexpected error: <type 'exceptions.Exception'> Traceback (most recent call last): File "/oppni/oppni.py", line 222, in run_oppni() File "/oppni/oppni.py", line 199, in run_oppni run_part_one(args.bids_dir, args.participant_label, task_group, args.output_dir, args.analysis_level ) File "/oppni/oppni.py", line 150, in run_part_one run_cmd(cmd) File "/oppni/oppni.py", line 67, in run_cmd raise Exception("Non zero return code: %d"%process.returncode) Exception: Non zero return code: 255

On 1 June 2017 at 11:06, Pradeep Reddy Raamana notifications@github.com wrote:

Actually, @chrisfilo https://github.com/chrisfilo has a better idea to make the installation of BIDS validator, part of OPPNI itself. This additional feature is being tested, and will update you in a bit.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/oppni/issues/13#issuecomment-305573645, or mute the thread https://github.com/notifications/unsubscribe-auth/ACSMC49uAbjfjoYcBvQpc-BUMlcMM-mlks5r_v3BgaJpZM4NtRoq .

raamana commented 7 years ago

Hi Lynne, thank you for trying it. We are doing some more internal tests to track the source of this error, and will update this app shortly with the latest code. Please wait for me to push these updates, so you give it another try. Thanks.

LJWilliams commented 7 years ago

Thank-you.

Lynne

On Jun 5, 2017, at 14:35, Pradeep Reddy Raamana notifications@github.com wrote:

Hi Lynne, thank you for trying it. We are doing some more internal tests to track the source of this error, and will update this app shortly with the latest code. Please wait for me to push these updates, so you give it another try. Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.