[Loris-dev] Upgrading to Loris 21 - new make file
Shen Wang
wangshen.mcin at gmail.com
Wed Aug 14 18:36:38 EDT 2019
Hi,Sotirios
In your special situation, there is a temporary fix.
step 1. sudo git stash
step 2. open webpack.config.js file
remove line 75 use: ['babel-loader', 'eslint-loader'],
save it.
step 3. sudo make
I hope this could help you to compile the js files.
On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> I forgot to mention that i had already moved my previous config file and
> re-executed the installation script.
>
> Στις Τετ, 14 Αυγ 2019 στις 3:26 μ.μ., ο/η Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> έγραψε:
>
>> Hi,
>>
>> Step 1 worked and the indentation errors were fixed. About step2 i added
>> all of these( there are more to include in the list) these to .eslintignore
>> which were reported to fail at being built, but they still appear on the
>> errors at the make_output file.
>>
>> /jsx/DynamicDataTable.js
>> /jsx/StaticDataTable.js
>> /jsx/MultiSelectDropdown.js
>> /jsx/Breadcrumbs.js
>> /jsx/Form.js
>> /jsx/Markdown.js
>> /modules/media/jsx/mediaIndex.js
>> /modules/issue_tracker/jsx/issueTrackerIndex.js
>> /modules/issue_tracker/jsx/index.js
>> /modules/candidate_parameters/jsx/CandidateParameters.js
>> /modules/configuration/jsx/SubprojectRelations.js
>> /modules/conflict_resolver/jsx/conflictResolverIndex.js
>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js
>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js
>> /modules/dataquery/jsx/react.tabs.js
>> /modules/document_repository/jsx/docIndex.js
>> /modules/instrument_builder/jsx/react.instrument_builder.js
>> /modules/imaging_uploader/jsx/index.js
>> /modules/datadict/jsx/dataDictIndex.js
>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js
>> /modules/new_profile/jsx/NewProfileIndex.js
>> /modules/examiner/jsx/examinerIndex.js
>> /modules/configuration/jsx/SubprojectRelations.js
>> /modules/data_team_helper/jsx/behavioural_qc_module.js
>> /modules/acknowledgements/jsx/acknowledgementsIndex.js
>> /modules/candidate_parameters/jsx/CandidateParameters.js
>> /modules/imaging_browser/jsx/ImagePanel.js
>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js
>>
>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js
>> /modules/genomic_browser/jsx/profileColumnFormatter.js
>> /modules/dataquery/jsx/react.tabs.js
>> /jsx/MultiSelectDropdown.js
>> /modules/mri_violations/jsx/columnFormatterUnresolved.js
>> /modules/dataquery/jsx/react.sidebar.js
>> /modules/dataquery/jsx/react.fieldselector.js
>> /modules/quality_control/jsx/qualityControlIndex.js
>> /modules/dataquery/jsx/react.paginator.js
>> /modules/instrument_builder/jsx/react.questions.js
>> /modules/dataquery/jsx/react.filterBuilder.js
>> /modules/conflict_resolver/jsx/conflictResolverIndex.js
>> /jsx/PaginationLinks.js
>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js
>> /modules/dataquery/jsx/react.app.js
>> /modules/candidate_list/jsx/onLoad.js
>> /jsx/Form.js
>> /modules/publication/jsx/publicationIndex.js
>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js
>> /modules/imaging_browser/jsx/imagingBrowserIndex.js
>> /modules/issue_tracker/jsx/issueTrackerIndex.js
>> /modules/survey_accounts/jsx/surveyAccountsIndex.js
>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js
>> /modules/instrument_manager/jsx/instrumentManagerIndex.js
>> /modules/media/jsx/mediaIndex.js
>> /modules/user_accounts/jsx/userAccountsIndex.js
>> /modules/help_editor/jsx/help_editor.js
>> /modules/dicom_archive/jsx/dicom_archive.js
>> /modules/mri_violations/jsx/columnFormatter.js
>> /modules/brainbrowser/jsx/Brainbrowser.js
>> /node_modules/babel-loader/lib/index.js
>> /modules/document_repository/jsx/editFormIndex.js
>>
>> Thanks
>>
>> Στις Τετ, 14 Αυγ 2019 στις 7:50 π.μ., ο/η Christine Rogers, Ms. <
>> christine.rogers at mcgill.ca> έγραψε:
>>
>>> Hi Shen and Sotirios - just a note,
>>>
>>> For the 21 release, it's best to run the install script without sudoing
>>> it.
>>>
>>> (Shen, I believe we discovered a minor issue with the sudo last week
>>> #5008)
>>>
>>> Best,
>>> Christine
>>>
>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang <wangshen.mcin at gmail.com>
>>> wrote:
>>>
>>>> Does it work? If still doesn’t work, try to remove project/config.xml
>>>> file. Do sudo ./install.sh again. To reinstall Loris again.
>>>>
>>>>
>>>> Shen Wang <wangshen.mcin at gmail.com>于2019年8月13日 周二下午9:02写道：
>>>>
>>>>> Hi Sotirios,
>>>>> step 1:
>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris
>>>>> step 2:
>>>>> put the rest error files under this line [# Ignore until ESLint is run
>>>>> ] in the .eslintignore file.
>>>>> step 3:
>>>>> sudo make
>>>>>
>>>>>
>>>>>
>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> I did the modifications, still there are errors.
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>> Στις Τετ, 14 Αυγ 2019 στις 3:22 π.μ., ο/η Shen Wang <
>>>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>> I saw your output file, the config issue is gone.
>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these indent
>>>>>>> issues.
>>>>>>> If it still has errors.
>>>>>>> Then try modify this file .eslintignore
>>>>>>> with this
>>>>>>>
>>>>>>> # Ignore until ESLint is run
>>>>>>>
>>>>>>> modules/*
>>>>>>>
>>>>>>> modules/dataquery/
>>>>>>>
>>>>>>> node_modules/*
>>>>>>>
>>>>>>> htdocs/js/components/*
>>>>>>>
>>>>>>> jsx/*
>>>>>>>
>>>>>>>
>>>>>>> # Ignore external libs
>>>>>>>
>>>>>>> htdocs/js/flot/*
>>>>>>>
>>>>>>> htdocs/js/jquery/*
>>>>>>>
>>>>>>> htdocs/js/jszip/*
>>>>>>>
>>>>>>> htdocs/js/modernizr/*
>>>>>>>
>>>>>>> htdocs/js/modules/*
>>>>>>>
>>>>>>> htdocs/js/react/*
>>>>>>>
>>>>>>> htdocs/js/shims/*
>>>>>>>
>>>>>>> htdocs/js/c3.min.js
>>>>>>>
>>>>>>> htdocs/js/d3.min.js
>>>>>>>
>>>>>>> htdocs/js/FileSaver.min.js
>>>>>>>
>>>>>>>
>>>>>>> then do sudo make.
>>>>>>> It should work.
>>>>>>> Regards
>>>>>>> Shen
>>>>>>>
>>>>>>>
>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>于2019年8月13日
>>>>>>> 周二下午7:54写道：
>>>>>>>
>>>>>>>> No, it didn't work, i also tried space/tabs because most of the
>>>>>>>> errors where about indentation, also there are some errors about React.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint
>>>>>>>> --init
>>>>>>>> ? How would you like to configure ESLint? Answer questions about
>>>>>>>> your style
>>>>>>>> ? Which version of ECMAScript do you use? ES2015
>>>>>>>> ? Are you using ES6 modules? Yes
>>>>>>>> ? Where will your code run? Browser
>>>>>>>> ? Do you use CommonJS? Yes
>>>>>>>> ? Do you use JSX? Yes
>>>>>>>> ? Do you use React? Yes
>>>>>>>> ? What style of indentation do you use? Spaces
>>>>>>>> ? What quotes do you use for strings? Single
>>>>>>>> ? What line endings do you use? Unix
>>>>>>>> ? Do you require semicolons? Yes
>>>>>>>> ? What format do you want your config file to be in? JSON
>>>>>>>> The config that you've selected requires the following dependencies:
>>>>>>>>
>>>>>>>> eslint-plugin-react at latest
>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris
>>>>>>>>
>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output
>>>>>>>> npm WARN The package prop-types is included as both a dev and
>>>>>>>> production dependency.
>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4
>>>>>>>> (node_modules/fsevents):
>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform
>>>>>>>> for fsevents at 1.2.4: wanted {"os":"darwin","arch":"any"} (current:
>>>>>>>> {"os":"linux","arch":"x64"})
>>>>>>>>
>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>> npm ERR! errno 2
>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>> npm ERR! Exit status 2
>>>>>>>> npm ERR!
>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script.
>>>>>>>> npm ERR! This is probably not a problem with npm. There is likely
>>>>>>>> additional logging output above.
>>>>>>>>
>>>>>>>> npm ERR! A complete log of this run can be found in:
>>>>>>>> npm ERR!
>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log
>>>>>>>>
>>>>>>>> Στις Τετ, 14 Αυγ 2019 στις 2:29 π.μ., ο/η Shen Wang <
>>>>>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>> When you do make command, please make sure with sudo at the
>>>>>>>>> beginning. [sudo make]
>>>>>>>>> If it still doesn't work for you.
>>>>>>>>> Then try the solutions below.
>>>>>>>>> solution 1:
>>>>>>>>> [image: 屏幕快照 2019-08-13 19.21.15.png]
>>>>>>>>> Regards
>>>>>>>>> Shen
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> I think that the files exists although i redownloaded the
>>>>>>>>>> eslintrc.json i checked others files that had similar errors.
>>>>>>>>>>
>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l
>>>>>>>>>> ./node_modules/eslint-loader/index.js
>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 Οκτ 26 1985
>>>>>>>>>> ./node_modules/eslint-loader/index.js
>>>>>>>>>>
>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json
>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 Αύγ 14 00:04
>>>>>>>>>> .eslintrc.json
>>>>>>>>>>
>>>>>>>>>> Maybe this can help
>>>>>>>>>>
>>>>>>>>>> Module build failed (from ./node_modules/eslint-loader/index.js):
>>>>>>>>>> SyntaxError: Cannot read config file:
>>>>>>>>>> /var/www/loris/.eslintrc.json
>>>>>>>>>> Error: Unexpected token < in JSON at position 6
>>>>>>>>>> at JSON.parse (<anonymous>)
>>>>>>>>>> at loadJSONConfigFile
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>>>>>>>>> at loadConfigFile
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>>>>>>>>> at loadFromDisk
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>>>>>>>>> at Object.load
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>>>>>>>>> at Config.getLocalConfigHierarchy
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>>>>>>>>> at Config.getConfigHierarchy
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>>>>>>>>> at Config.getConfigVector
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>>>>>>>>> at Config.getConfig
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>>>>>>>>> at processText
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>>>>>>>>> at CLIEngine.executeOnText
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>>>>>>>>> at lint
>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>>>>>>>>> at Object.module.exports
>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>>>>>>>>>
>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js
>>>>>>>>>> Module build failed (from
>>>>>>>>>> ./node_modules/eslint-loader/index.js):
>>>>>>>>>> SyntaxError: Cannot read config file:
>>>>>>>>>> /var/www/loris/.eslintrc.json
>>>>>>>>>> Error: Unexpected token < in JSON at position 6
>>>>>>>>>> at JSON.parse (<anonymous>)
>>>>>>>>>> at loadJSONConfigFile
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>>>>>>>>> at loadConfigFile
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>>>>>>>>> at loadFromDisk
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>>>>>>>>> at Object.load
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>>>>>>>>> at Config.getLocalConfigHierarchy
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>>>>>>>>> at Config.getConfigHierarchy
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>>>>>>>>> at Config.getConfigVector
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>>>>>>>>> at Config.getConfig
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>>>>>>>>> at processText
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>>>>>>>>> at CLIEngine.executeOnText
>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>>>>>>>>> at lint
>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>>>>>>>>> at Object.module.exports
>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 13 Αυγ 2019 στις 11:52 μ.μ., ο/η John Saigle <
>>>>>>>>>> john.saigle at mcin.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> HI Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> The make_output.txt file shows webpack failing because it can't
>>>>>>>>>>> find the ESLint config file.
>>>>>>>>>>>
>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists within
>>>>>>>>>>> your loris root directory (usually `/var/www/loris/`)? When I delete my
>>>>>>>>>>> file I get the same errors as you.
>>>>>>>>>>>
>>>>>>>>>>> If you find that it's missing, you can make a local copy with
>>>>>>>>>>> the contents found here:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json
>>>>>>>>>>>
>>>>>>>>>>> Once you know it exists, try running `make` again.
>>>>>>>>>>>
>>>>>>>>>>> Let us know if that moves you forward.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> John
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>> I executed the commands for the node and now i am get the
>>>>>>>>>>>> followings:
>>>>>>>>>>>>
>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output
>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and
>>>>>>>>>>>> production dependency.
>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4
>>>>>>>>>>>> (node_modules/fsevents):
>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported
>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted
>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
>>>>>>>>>>>>
>>>>>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>>>>>> npm ERR! errno 2
>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>>>>>> npm ERR! Exit status 2
>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script.
>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is
>>>>>>>>>>>> likely additional logging output above.
>>>>>>>>>>>>
>>>>>>>>>>>> npm ERR! A complete log of this run can be found in:
>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log
>>>>>>>>>>>> make: *** [javascript] Error 2
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Δευ, 12 Αυγ 2019 στις 10:19 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to 21
>>>>>>>>>>>>> whose version of node doesn't work well with webpack, due to updated
>>>>>>>>>>>>> packages they're missing.
>>>>>>>>>>>>> If so, update your node :
>>>>>>>>>>>>>
>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>>>>>>>>>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>
>>>>>>>>>>>>> Let us know how that goes -- please send us output from the
>>>>>>>>>>>>> same log if any issues.
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have
>>>>>>>>>>>>>> still 74GB available.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h
>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on
>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev
>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run
>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% /
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as
>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function,
>>>>>>>>>>>>>> class) not yet supported outside strict mode"
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Πέμ, 8 Αυγ 2019 στις 4:32 μ.μ., ο/η Dave MacFarlane <
>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error
>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of
>>>>>>>>>>>>>>> disk space?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I runned make and also included the file it reports at the
>>>>>>>>>>>>>>>> end.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make
>>>>>>>>>>>>>>>> npm install
>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>>>>>>>>>> /chokidar/fsevents:
>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system
>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9
>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents:
>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating system
>>>>>>>>>>>>>>>> or architecture: fsevents at 1.2.9
>>>>>>>>>>>>>>>> npm run compile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris
>>>>>>>>>>>>>>>> > webpack
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86
>>>>>>>>>>>>>>>> let notify =
>>>>>>>>>>>>>>>> ^^^
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const,
>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode
>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16)
>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25)
>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10)
>>>>>>>>>>>>>>>> at Module.load (module.js:344:32)
>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12)
>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10)
>>>>>>>>>>>>>>>> at startup (node.js:136:18)
>>>>>>>>>>>>>>>> at node.js:966:3
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic
>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run"
>>>>>>>>>>>>>>>> "compile"
>>>>>>>>>>>>>>>> npm ERR! node v4.2.6
>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2
>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>>>>>>>>>> npm ERR! Exit status 1
>>>>>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script
>>>>>>>>>>>>>>>> 'webpack'.
>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of node.js
>>>>>>>>>>>>>>>> and npm installed.
>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with the
>>>>>>>>>>>>>>>> loris package,
>>>>>>>>>>>>>>>> npm ERR! not with npm itself.
>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system:
>>>>>>>>>>>>>>>> npm ERR! webpack
>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an issue
>>>>>>>>>>>>>>>> for this project with:
>>>>>>>>>>>>>>>> npm ERR! npm bugs loris
>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their info
>>>>>>>>>>>>>>>> via:
>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris
>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output above.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any support
>>>>>>>>>>>>>>>> request:
>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log
>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed
>>>>>>>>>>>>>>>> make: *** [javascript] Error 1
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Τετ, 7 Αυγ 2019 στις 5:41 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps?
>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times)
>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c directory
>>>>>>>>>>>>>>>>> (this will clear the template cache - do Not touch smarty/templates/)
>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces the
>>>>>>>>>>>>>>>>> composer commands used in previous releases to update your dependencies)
>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt)
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference you
>>>>>>>>>>>>>>>>> see after, with your logs. A
>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these
>>>>>>>>>>>>>>>>> Troubleshooting Queries
>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>)
>>>>>>>>>>>>>>>>> if you're still seeing front-end issues.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat
>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log
>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice]
>>>>>>>>>>>>>>>>>> [pid 1267] AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured --
>>>>>>>>>>>>>>>>>> resuming normal operations
>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid
>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2'
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty
>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 Ιούν 28 14:09
>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The only non-blank pages are:
>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all,
>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and
>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for
>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue."
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τρί, 6 Αυγ 2019 στις 10:13 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community --
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a
>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new
>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of
>>>>>>>>>>>>>>>>>>> using *composer* commands).
>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page
>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Updating-your-LORIS>
>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to
>>>>>>>>>>>>>>>>>>> run.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If your current version is not the last release (20.3),
>>>>>>>>>>>>>>>>>>> it's still important to upgrade to each minor release increment (e.g. 20.2,
>>>>>>>>>>>>>>>>>>> 20.3) before making the leap to 21.0.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try
>>>>>>>>>>>>>>>>>>> clearing your cache.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes?
>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know.
>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is content
>>>>>>>>>>>>>>>>>>>> visible, and on which pages/modules is content not visible for you?
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios,
>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've checked
>>>>>>>>>>>>>>>>>>>>> that your /var/www/loris/project/config.xml file get populated properly.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing in
>>>>>>>>>>>>>>>>>>>>> your apache error log file, and your config paths and we can see what's
>>>>>>>>>>>>>>>>>>>>> happening with your front end --
>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries
>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying
>>>>>>>>>>>>>>>>>>>>> fully.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo
>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21
>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps.
>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was:
>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them to my
>>>>>>>>>>>>>>>>>>>>>> existing /vaw/www/loris folder.
>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and then composer
>>>>>>>>>>>>>>>>>>>>>> dump-autoload as mentioned here
>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS
>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and
>>>>>>>>>>>>>>>>>>>>>> because LORIS already existed i moved a .config file, then re-executed the
>>>>>>>>>>>>>>>>>>>>>> install.sh successfully
>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and i
>>>>>>>>>>>>>>>>>>>>>> executed the installdb.php
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on a
>>>>>>>>>>>>>>>>>>>>>>> fresh root path / VM or might some of your old system setting still apply?
>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade, did
>>>>>>>>>>>>>>>>>>>>>>> you follow the Upgrade steps in the Release Notes, from both repos?)
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently split (MRI
>>>>>>>>>>>>>>>>>>>>>>> pr339 <https://github.com/aces/Loris-MRI/pull/339>) split
>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range
>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version
>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed
>>>>>>>>>>>>>>>>>>>>>>> to ensure they match.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the
>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the
>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm
>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column
>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch()
>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986.
>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in
>>>>>>>>>>>>>>>>>>>>>>>>> numeric gt (>) at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995.
>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column
>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562.
>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21 this
>>>>>>>>>>>>>>>>>>>>>>>>>> week with some major new features and cleanup -- especially if you are
>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the
>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/releases/tag/v21.0.0>
>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0>
>>>>>>>>>>>>>>>>>>>>>>>>>> repos.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty
>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues :
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a
>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't
>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with entries
>>>>>>>>>>>>>>>>>>>>>>>>>> for t1, t2, fMRI and DTI (Insert statements for
>>>>>>>>>>>>>>>>>>>>>>>>>> 21 release branch are here
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>
>>>>>>>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and
>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter the
>>>>>>>>>>>>>>>>>>>>>>>>>> scans displayed as you move to the next page (View Session), instead of
>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session :
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md>
>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy)
>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing has
>>>>>>>>>>>>>>>>>>>>>>>>>> been performed on the scan (it's raw data),
>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that
>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display
>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session,
>>>>>>>>>>>>>>>>>>>>>>>>>> e.g.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments --
>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans (matched
>>>>>>>>>>>>>>>>>>>>>>>>>> to the mri_protocol table), you'll be able to use the Imaging Browser's
>>>>>>>>>>>>>>>>>>>>>>>>>> View Session subpage to enter/view QC comments on each volume, or for each
>>>>>>>>>>>>>>>>>>>>>>>>>> visit.
>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database, and
>>>>>>>>>>>>>>>>>>>>>>>>>> linked to each scan. (Table name:
>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments)
>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the
>>>>>>>>>>>>>>>>>>>>>>>>>> session.)
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup - please
>>>>>>>>>>>>>>>>>>>>>>>>>> see the Imaging Setup guide
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md>
>>>>>>>>>>>>>>>>>>>>>>>>>> -
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video
>>>>>>>>>>>>>>>>>>>>>>>>>> <https://www.youtube.com/watch?v=HDWC6RUbI6A> can
>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at
>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00
>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many
>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries in
>>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table -
>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this patient
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it
>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No results
>>>>>>>>>>>>>>>>>>>>>>>>>>> ( neither on resolved / not resolved ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record
>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see the
>>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol Name which i think is the acquisition we wanted?
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the
>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where
>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored?
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit labels. To follow up on your last few emails:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample
>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>> label format is important: V01, v01, V1, 01 -- whichever you select to use
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is fine; we use V01 by default across all documentation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> tools/ directory so that a back-end administrator can reset any front-end
>>>>>>>>>>>>>>>>>>>>>>>>>>>> user password, including Admin. (See info on setting up / resetting User
>>>>>>>>>>>>>>>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered -- due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol) in you Dicom header was not matched to any scan listed in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol database table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted").
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here)
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/tree/minor/modules/mri_violations>will show
>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch --
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find
>>>>>>>>>>>>>>>>>>>>>>>>>>>> your scan and click the link "Could not identify scan type" -- in the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>> subpage you can compare the scan's actual parameters against the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>>> values or perhaps ensure your DICOMs are labelled consistently.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can
>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label disappeared.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also something i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> found.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the AcquisitionProtocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> hash and by deleting the rows from the login_history i was able to login.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 =
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had suggested but it appears that this problem hasn't been resolved yet.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Logging to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the fact that your psc table does not have the MRI_alias populated for the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC site. Running the following query in the mysql database should fix this:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did the modifications you suggested, i still get the "no mincs inserted"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> just need to update a few config settings from the frontend in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module (under the Admin menu).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module and update the "LORIS-MRI code" config setting to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Configuration module and update the "Loris-MRI Data Directory" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be in the environment file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> π.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command =
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> example: it was repeating a pattern and had LORIS instead of loris ( i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setting not set (based on the first error message you got when running it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time). You need to set a value for "Loris-MRI Data Directory" in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Config module under the Imaging pipeline section (from what I can see,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it would be /data/loris/data/ for your setup).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already been run with tarchiveID: 7.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion pipeline, please run tarchiveLoader from a terminal as follows:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 5:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creation, if you execute the following steps, the pipeline should be able
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to create candidates:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the LORIS server instead of uploading it via the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you did until now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> automatically created.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be considered for inserting into the database: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 3:38
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the log.txt file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM header does not start with DCC0000_258024_V1 from the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate profile i have to create a new one each time before i try to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom with a blank studyUID, maybe someone accidentally removed it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> offer a script to remove all the entries and files specific to an upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, this release is not yet out. Hopefully in the next few weeks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case is particular and that you just want to start with a clean database,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the following deletes should work (hopefully I won't forget any tables):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; #
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (if you played with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID="scanner";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also delete entries in the session and candidate table too?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the profile of a patient ( are the patients stored in the candidate table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> because i can't see the ghosts ), because will it automatically be created
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> when importing a dicom?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question, otherwise, don't hesitate to let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seem cumbersome but they are here to ensure that the files inserted are all
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers to your questions will be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you will find the initial answer I gave Sotirios below. I forgot to cc the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev in my earlier reply...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019 στις
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 12:02 π.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Since your email was already organized in points, I will reply directly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> below your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank on the header?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> used in our pipeline at the moment to check whether a DICOM study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> why the StudyUID is blank in the DICOM headers in your DICOM files? Did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> they go through some processes before upload to LORIS?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a non-phanton case i need a 'Visit Label'. Is there already a script that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create a new visit label for a specific Candidate, so i can provide it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as input afterwards to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts will create a V02 visit for MTL0123 if the PatientName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field for the dataset is MTL0123_456789_V02 with Stage marked as "Not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Started".
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to create the visit for the candidate, you have to make sure that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the visit label of your projects were inserted in the Visit_Windows
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table* (otherwise, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit will never be created as they were not specified as being part of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list of visit label to expect). So in the example above, you should have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC file, provided you have at least the following information:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files or DICOM archive path from which those MINC files were
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the same uploadID or TarchiveID, then you could run a loop in bash
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> calling the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like this for files deriving from uploadID=1:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> while read f; do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> prod -uploadID 1 -mincPath $f; done
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Shen Wang
>>>>>>>>> Loris <https://github.com/aces/Loris> Developer
>>>>>>>>> Montreal Neurological Institute
>>>>>>>>> McGill University
>>>>>>>>>
>>>>>>>>>
>>>>>
>>>>> --
>>>>> Shen Wang
>>>>> Loris <https://github.com/aces/Loris> Developer
>>>>> Montreal Neurological Institute
>>>>> McGill University
>>>>>
>>>>> --
>>>> Shen Wang
>>>> Loris <https://github.com/aces/Loris> Developer
>>>> Montreal Neurological Institute
>>>> McGill University
>>>>
>>>> _______________________________________________
>>>> Loris-dev mailing list
>>>> Loris-dev at bic.mni.mcgill.ca
>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>
--
Shen Wang
Loris <https://github.com/aces/Loris> Developer
Montreal Neurological Institute
McGill University
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