[Loris-dev] Upgrading to Loris 21 - new make file
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Thu Aug 15 14:45:17 EDT 2019
I attached the sudo make output.
Στις Πέμ, 15 Αυγ 2019 στις 9:36 μ.μ., ο/η Shen Wang <wangshen.mcin at gmail.com>
έγραψε:
> Hi,
> You don't need to run install.sh this time. Redownload the missing file,
> then do sudo make.
> If it still have indent and no-def errors, then remove the lines which I
> told you from webpack.config.js, then try do
> sudo make again.
>
>
> On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi,
>>
>> should i try to redownload the files from
>> https://github.com/aces/Loris/tree/major and execute the install.sh? I
>> find it weird that i am missing some files.
>>
>> Thanks
>>
>> Στις Πέμ, 15 Αυγ 2019 στις 9:17 μ.μ., ο/η Shen Wang <
>> wangshen.mcin at gmail.com> έγραψε:
>>
>>> Hi Sotirios,
>>> It seems like you are missing this file. [ .babelrc]
>>> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc
>>> step 2: sudo vi webpack.config.js
>>> remove these lines
>>>
>>> { test: /\.js$/,
>>>
>>> exclude: /node_modules/,
>>>
>>> // use: ['babel-loader', 'eslint-loader'],
>>>
>>> },
>>>
>>> step 3: sudo make
>>>
>>>
>>>
>>> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Shen,
>>>>
>>>> That didn't work either. Also i had removed the git files because i was
>>>> getting this error when i used make:
>>>>
>>>> "git describe --tags --always > VERSION
>>>> fatal: Not a git repository (or any of the parent directories): .git
>>>> Makefile:8: recipe for target 'VERSION' failed
>>>> make: *** [VERSION] Error 128"
>>>>
>>>> Thanks
>>>>
>>>> Στις Πέμ, 15 Αυγ 2019 στις 1:36 π.μ., ο/η Shen Wang <
>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>
>>>>> 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
>>>>>
>>>>>
>>>
>>> --
>>> 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
>
>
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