[Loris-dev] Upgrading to Loris 21 - new make file

Thu Aug 15 14:28:35 EDT 2019

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
>
>
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