[Loris-dev] Upgrading to Loris 21 - new make file
Shen Wang
wangshen.mcin at gmail.com
Thu Aug 15 14:36:27 EDT 2019
Hi,
You don't need to run install.sh this time. Redownload the missing file,
then do sudo make.
If it still have indent and no-def errors, then remove the lines which I
told you from webpack.config.js, then try do
sudo make again.
On Thu, 15 Aug 2019 at 14:28, Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> Hi,
>
> should i try to redownload the files from
> https://github.com/aces/Loris/tree/major and execute the install.sh? I
> find it weird that i am missing some files.
>
> Thanks
>
> Στις Πέμ, 15 Αυγ 2019 στις 9:17 μ.μ., ο/η Shen Wang <
> wangshen.mcin at gmail.com> έγραψε:
>
>> Hi Sotirios,
>> It seems like you are missing this file. [ .babelrc]
>> step 1: copy from https://github.com/aces/Loris/blob/major/.babelrc
>> step 2: sudo vi webpack.config.js
>> remove these lines
>>
>> { test: /\.js$/,
>>
>> exclude: /node_modules/,
>>
>> // use: ['babel-loader', 'eslint-loader'],
>>
>> },
>>
>> step 3: sudo make
>>
>>
>>
>> On Wed, 14 Aug 2019 at 18:52, Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Shen,
>>>
>>> That didn't work either. Also i had removed the git files because i was
>>> getting this error when i used make:
>>>
>>> "git describe --tags --always > VERSION
>>> fatal: Not a git repository (or any of the parent directories): .git
>>> Makefile:8: recipe for target 'VERSION' failed
>>> make: *** [VERSION] Error 128"
>>>
>>> Thanks
>>>
>>> Στις Πέμ, 15 Αυγ 2019 στις 1:36 π.μ., ο/η Shen Wang <
>>> wangshen.mcin at gmail.com> έγραψε:
>>>
>>>> Hi,Sotirios
>>>> In your special situation, there is a temporary fix.
>>>> step 1. sudo git stash
>>>> step 2. open webpack.config.js file
>>>> remove line 75 use: ['babel-loader', 'eslint-loader'],
>>>> save it.
>>>> step 3. sudo make
>>>>
>>>> I hope this could help you to compile the js files.
>>>>
>>>>
>>>>
>>>> On Wed, 14 Aug 2019 at 08:28, Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> I forgot to mention that i had already moved my previous config file
>>>>> and re-executed the installation script.
>>>>>
>>>>> Στις Τετ, 14 Αυγ 2019 στις 3:26 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Step 1 worked and the indentation errors were fixed. About step2 i
>>>>>> added all of these( there are more to include in the list) these to
>>>>>> .eslintignore which were reported to fail at being built, but they still
>>>>>> appear on the errors at the make_output file.
>>>>>>
>>>>>> /jsx/DynamicDataTable.js
>>>>>> /jsx/StaticDataTable.js
>>>>>> /jsx/MultiSelectDropdown.js
>>>>>> /jsx/Breadcrumbs.js
>>>>>> /jsx/Form.js
>>>>>> /jsx/Markdown.js
>>>>>> /modules/media/jsx/mediaIndex.js
>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js
>>>>>> /modules/issue_tracker/jsx/index.js
>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js
>>>>>> /modules/configuration/jsx/SubprojectRelations.js
>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js
>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js
>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js
>>>>>> /modules/dataquery/jsx/react.tabs.js
>>>>>> /modules/document_repository/jsx/docIndex.js
>>>>>> /modules/instrument_builder/jsx/react.instrument_builder.js
>>>>>> /modules/imaging_uploader/jsx/index.js
>>>>>> /modules/datadict/jsx/dataDictIndex.js
>>>>>> /modules/bvl_feedback/jsx/react.behavioural_feedback_panel.js
>>>>>> /modules/new_profile/jsx/NewProfileIndex.js
>>>>>> /modules/examiner/jsx/examinerIndex.js
>>>>>> /modules/configuration/jsx/SubprojectRelations.js
>>>>>> /modules/data_team_helper/jsx/behavioural_qc_module.js
>>>>>> /modules/acknowledgements/jsx/acknowledgementsIndex.js
>>>>>> /modules/candidate_parameters/jsx/CandidateParameters.js
>>>>>> /modules/imaging_browser/jsx/ImagePanel.js
>>>>>> /modules/mri_violations/jsx/mri_protocol_violations_columnFormatter.js
>>>>>>
>>>>>> /modules/mri_violations/jsx/mri_protocol_check_violations_columnFormatter.js
>>>>>> /modules/genomic_browser/jsx/profileColumnFormatter.js
>>>>>> /modules/dataquery/jsx/react.tabs.js
>>>>>> /jsx/MultiSelectDropdown.js
>>>>>> /modules/mri_violations/jsx/columnFormatterUnresolved.js
>>>>>> /modules/dataquery/jsx/react.sidebar.js
>>>>>> /modules/dataquery/jsx/react.fieldselector.js
>>>>>> /modules/quality_control/jsx/qualityControlIndex.js
>>>>>> /modules/dataquery/jsx/react.paginator.js
>>>>>> /modules/instrument_builder/jsx/react.questions.js
>>>>>> /modules/dataquery/jsx/react.filterBuilder.js
>>>>>> /modules/conflict_resolver/jsx/conflictResolverIndex.js
>>>>>> /jsx/PaginationLinks.js
>>>>>> /modules/conflict_resolver/jsx/resolvedConflictsIndex.js
>>>>>> /modules/dataquery/jsx/react.app.js
>>>>>> /modules/candidate_list/jsx/onLoad.js
>>>>>> /jsx/Form.js
>>>>>> /modules/publication/jsx/publicationIndex.js
>>>>>> /modules/server_processes_manager/jsx/server_processes_managerIndex.js
>>>>>> /modules/imaging_browser/jsx/imagingBrowserIndex.js
>>>>>> /modules/issue_tracker/jsx/issueTrackerIndex.js
>>>>>> /modules/survey_accounts/jsx/surveyAccountsIndex.js
>>>>>> /modules/data_integrity_flag/jsx/dataIntegrityFlagIndex.js
>>>>>> /modules/instrument_manager/jsx/instrumentManagerIndex.js
>>>>>> /modules/media/jsx/mediaIndex.js
>>>>>> /modules/user_accounts/jsx/userAccountsIndex.js
>>>>>> /modules/help_editor/jsx/help_editor.js
>>>>>> /modules/dicom_archive/jsx/dicom_archive.js
>>>>>> /modules/mri_violations/jsx/columnFormatter.js
>>>>>> /modules/brainbrowser/jsx/Brainbrowser.js
>>>>>> /node_modules/babel-loader/lib/index.js
>>>>>> /modules/document_repository/jsx/editFormIndex.js
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Στις Τετ, 14 Αυγ 2019 στις 7:50 π.μ., ο/η Christine Rogers, Ms. <
>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>
>>>>>>> Hi Shen and Sotirios - just a note,
>>>>>>>
>>>>>>> For the 21 release, it's best to run the install script without
>>>>>>> sudoing it.
>>>>>>>
>>>>>>> (Shen, I believe we discovered a minor issue with the sudo last week
>>>>>>> #5008)
>>>>>>>
>>>>>>> Best,
>>>>>>> Christine
>>>>>>>
>>>>>>> On Tue, Aug 13, 2019 at 9:22 PM Shen Wang <wangshen.mcin at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Does it work? If still doesn’t work, try to remove
>>>>>>>> project/config.xml file. Do sudo ./install.sh again. To reinstall Loris
>>>>>>>> again.
>>>>>>>>
>>>>>>>>
>>>>>>>> Shen Wang <wangshen.mcin at gmail.com>于2019年8月13日 周二下午9:02写道：
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>> step 1:
>>>>>>>>> sudo ./node_modules/.bin/eslint --fix /var/www/loris
>>>>>>>>> step 2:
>>>>>>>>> put the rest error files under this line [# Ignore until ESLint
>>>>>>>>> is run] in the .eslintignore file.
>>>>>>>>> step 3:
>>>>>>>>> sudo make
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, 13 Aug 2019 at 20:34, Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> I did the modifications, still there are errors.
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Στις Τετ, 14 Αυγ 2019 στις 3:22 π.μ., ο/η Shen Wang <
>>>>>>>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>> I saw your output file, the config issue is gone.
>>>>>>>>>>> you can use [sudo npm run lintfix:javascript ] to fix these
>>>>>>>>>>> indent issues.
>>>>>>>>>>> If it still has errors.
>>>>>>>>>>> Then try modify this file .eslintignore
>>>>>>>>>>> with this
>>>>>>>>>>>
>>>>>>>>>>> # Ignore until ESLint is run
>>>>>>>>>>>
>>>>>>>>>>> modules/*
>>>>>>>>>>>
>>>>>>>>>>> modules/dataquery/
>>>>>>>>>>>
>>>>>>>>>>> node_modules/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/components/*
>>>>>>>>>>>
>>>>>>>>>>> jsx/*
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> # Ignore external libs
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/flot/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/jquery/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/jszip/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/modernizr/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/modules/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/react/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/shims/*
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/c3.min.js
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/d3.min.js
>>>>>>>>>>>
>>>>>>>>>>> htdocs/js/FileSaver.min.js
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> then do sudo make.
>>>>>>>>>>> It should work.
>>>>>>>>>>> Regards
>>>>>>>>>>> Shen
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>于2019年8月13日
>>>>>>>>>>> 周二下午7:54写道：
>>>>>>>>>>>
>>>>>>>>>>>> No, it didn't work, i also tried space/tabs because most of the
>>>>>>>>>>>> errors where about indentation, also there are some errors about React.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ./node_modules/.bin/eslint
>>>>>>>>>>>> --init
>>>>>>>>>>>> ? How would you like to configure ESLint? Answer questions
>>>>>>>>>>>> about your style
>>>>>>>>>>>> ? Which version of ECMAScript do you use? ES2015
>>>>>>>>>>>> ? Are you using ES6 modules? Yes
>>>>>>>>>>>> ? Where will your code run? Browser
>>>>>>>>>>>> ? Do you use CommonJS? Yes
>>>>>>>>>>>> ? Do you use JSX? Yes
>>>>>>>>>>>> ? Do you use React? Yes
>>>>>>>>>>>> ? What style of indentation do you use? Spaces
>>>>>>>>>>>> ? What quotes do you use for strings? Single
>>>>>>>>>>>> ? What line endings do you use? Unix
>>>>>>>>>>>> ? Do you require semicolons? Yes
>>>>>>>>>>>> ? What format do you want your config file to be in? JSON
>>>>>>>>>>>> The config that you've selected requires the following
>>>>>>>>>>>> dependencies:
>>>>>>>>>>>>
>>>>>>>>>>>> eslint-plugin-react at latest
>>>>>>>>>>>> Successfully created .eslintrc.json file in /var/www/loris
>>>>>>>>>>>>
>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo make > sudo_make_output
>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev and
>>>>>>>>>>>> production dependency.
>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.4
>>>>>>>>>>>> (node_modules/fsevents):
>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported
>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted
>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
>>>>>>>>>>>>
>>>>>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>>>>>> npm ERR! errno 2
>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>>>>>> npm ERR! Exit status 2
>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script.
>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is
>>>>>>>>>>>> likely additional logging output above.
>>>>>>>>>>>>
>>>>>>>>>>>> npm ERR! A complete log of this run can be found in:
>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T23_40_58_841Z-debug.log
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τετ, 14 Αυγ 2019 στις 2:29 π.μ., ο/η Shen Wang <
>>>>>>>>>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>> When you do make command, please make sure with sudo at the
>>>>>>>>>>>>> beginning. [sudo make]
>>>>>>>>>>>>> If it still doesn't work for you.
>>>>>>>>>>>>> Then try the solutions below.
>>>>>>>>>>>>> solution 1:
>>>>>>>>>>>>> [image: 屏幕快照 2019-08-13 19.21.15.png]
>>>>>>>>>>>>> Regards
>>>>>>>>>>>>> Shen
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, 13 Aug 2019 at 17:22, Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I think that the files exists although i redownloaded the
>>>>>>>>>>>>>> eslintrc.json i checked others files that had similar errors.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l
>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js
>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 6463 Οκτ 26 1985
>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ ls -l .eslintrc.json
>>>>>>>>>>>>>> -rw-rw-r-- 1 lorisadmin lorisadmin 84530 Αύγ 14 00:04
>>>>>>>>>>>>>> .eslintrc.json
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Maybe this can help
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Module build failed (from
>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js):
>>>>>>>>>>>>>> SyntaxError: Cannot read config file:
>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json
>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6
>>>>>>>>>>>>>> at JSON.parse (<anonymous>)
>>>>>>>>>>>>>> at loadJSONConfigFile
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>>>>>>>>>>>>> at loadConfigFile
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>>>>>>>>>>>>> at loadFromDisk
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>>>>>>>>>>>>> at Object.load
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>>>>>>>>>>>>> at Config.getConfigHierarchy
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>>>>>>>>>>>>> at Config.getConfigVector
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>>>>>>>>>>>>> at Config.getConfig
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>>>>>>>>>>>>> at processText
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>>>>>>>>>>>>> at CLIEngine.executeOnText
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>>>>>>>>>>>>> at lint
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>>>>>>>>>>>>> at Object.module.exports
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ERROR in ./modules/imaging_uploader/jsx/index.js
>>>>>>>>>>>>>> Module build failed (from
>>>>>>>>>>>>>> ./node_modules/eslint-loader/index.js):
>>>>>>>>>>>>>> SyntaxError: Cannot read config file:
>>>>>>>>>>>>>> /var/www/loris/.eslintrc.json
>>>>>>>>>>>>>> Error: Unexpected token < in JSON at position 6
>>>>>>>>>>>>>> at JSON.parse (<anonymous>)
>>>>>>>>>>>>>> at loadJSONConfigFile
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:114:21)
>>>>>>>>>>>>>> at loadConfigFile
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:230:26)
>>>>>>>>>>>>>> at loadFromDisk
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:500:18)
>>>>>>>>>>>>>> at Object.load
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config/config-file.js:564:20)
>>>>>>>>>>>>>> at Config.getLocalConfigHierarchy
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:227:44)
>>>>>>>>>>>>>> at Config.getConfigHierarchy
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:179:43)
>>>>>>>>>>>>>> at Config.getConfigVector
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:286:21)
>>>>>>>>>>>>>> at Config.getConfig
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/config.js:329:29)
>>>>>>>>>>>>>> at processText
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:162:33)
>>>>>>>>>>>>>> at CLIEngine.executeOnText
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint/lib/cli-engine.js:596:17)
>>>>>>>>>>>>>> at lint
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:237:17)
>>>>>>>>>>>>>> at Object.module.exports
>>>>>>>>>>>>>> (/var/www/loris/node_modules/eslint-loader/index.js:232:21)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Τρί, 13 Αυγ 2019 στις 11:52 μ.μ., ο/η John Saigle <
>>>>>>>>>>>>>> john.saigle at mcin.ca> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> HI Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The make_output.txt file shows webpack failing because it
>>>>>>>>>>>>>>> can't find the ESLint config file.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Can you confirm whether the file `.eslintrc.json` exists
>>>>>>>>>>>>>>> within your loris root directory (usually `/var/www/loris/`)? When I delete
>>>>>>>>>>>>>>> my file I get the same errors as you.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> If you find that it's missing, you can make a local copy
>>>>>>>>>>>>>>> with the contents found here:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/e26a6ad49a73fcffef0cd73bb600c4d17b200b62/.eslintrc.json
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Once you know it exists, try running `make` again.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Let us know if that moves you forward.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>> John
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Aug 13, 2019 at 2:21 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>> I executed the commands for the node and now i am get the
>>>>>>>>>>>>>>>> followings:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make > ~/make_output
>>>>>>>>>>>>>>>> npm WARN The package prop-types is included as both a dev
>>>>>>>>>>>>>>>> and production dependency.
>>>>>>>>>>>>>>>> npm WARN optional SKIPPING OPTIONAL DEPENDENCY:
>>>>>>>>>>>>>>>> fsevents at 1.2.4 (node_modules/fsevents):
>>>>>>>>>>>>>>>> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported
>>>>>>>>>>>>>>>> platform for fsevents at 1.2.4: wanted
>>>>>>>>>>>>>>>> {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>>>>>>>>>> npm ERR! errno 2
>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>>>>>>>>>> npm ERR! Exit status 2
>>>>>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script.
>>>>>>>>>>>>>>>> npm ERR! This is probably not a problem with npm. There is
>>>>>>>>>>>>>>>> likely additional logging output above.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> npm ERR! A complete log of this run can be found in:
>>>>>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>>>>>> /home/lorisadmin/.npm/_logs/2019-08-13T18_12_05_378Z-debug.log
>>>>>>>>>>>>>>>> make: *** [javascript] Error 2
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Δευ, 12 Αυγ 2019 στις 10:19 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> We've seen some users installing LORIS 21 or upgrading to
>>>>>>>>>>>>>>>>> 21 whose version of node doesn't work well with webpack, due to updated
>>>>>>>>>>>>>>>>> packages they're missing.
>>>>>>>>>>>>>>>>> If so, update your node :
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Let us know how that goes -- please send us output from
>>>>>>>>>>>>>>>>> the same log if any issues.
>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 2:38 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> It's not a disk space issue, as you can see below i have
>>>>>>>>>>>>>>>>>> still 74GB available.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ df -h
>>>>>>>>>>>>>>>>>> Filesystem Size Used Avail Use% Mounted on
>>>>>>>>>>>>>>>>>> udev 2,9G 0 2,9G 0% /dev
>>>>>>>>>>>>>>>>>> tmpfs 597M 8,6M 588M 2% /run
>>>>>>>>>>>>>>>>>> /dev/sda1 98G 19G 74G 21% /
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Maybe we have to pass a flag to get into strict mode? as
>>>>>>>>>>>>>>>>>> stated "SyntaxError: Block-scoped declarations (let, const, function,
>>>>>>>>>>>>>>>>>> class) not yet supported outside strict mode"
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Πέμ, 8 Αυγ 2019 στις 4:32 μ.μ., ο/η Dave MacFarlane <
>>>>>>>>>>>>>>>>>> dave.macfarlane at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> It looks like the javascript snippet shown in the error
>>>>>>>>>>>>>>>>>>> message when trying to compile the js is truncated. Have you run out of
>>>>>>>>>>>>>>>>>>> disk space?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I runned make and also included the file it reports at
>>>>>>>>>>>>>>>>>>>> the end.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ make
>>>>>>>>>>>>>>>>>>>> npm install
>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>>>>>>>>>>>>>> /chokidar/fsevents:
>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating
>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9
>>>>>>>>>>>>>>>>>>>> npm WARN optional Skipping failed optional dependency
>>>>>>>>>>>>>>>>>>>> /watchpack/chokidar/fsevents:
>>>>>>>>>>>>>>>>>>>> npm WARN notsup Not compatible with your operating
>>>>>>>>>>>>>>>>>>>> system or architecture: fsevents at 1.2.9
>>>>>>>>>>>>>>>>>>>> npm run compile
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> > loris at 1.0.0 compile /var/www/loris
>>>>>>>>>>>>>>>>>>>> > webpack
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> /var/www/loris/node_modules/webpack/bin/webpack.js:86
>>>>>>>>>>>>>>>>>>>> let notify =
>>>>>>>>>>>>>>>>>>>> ^^^
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> SyntaxError: Block-scoped declarations (let, const,
>>>>>>>>>>>>>>>>>>>> function, class) not yet supported outside strict mode
>>>>>>>>>>>>>>>>>>>> at exports.runInThisContext (vm.js:53:16)
>>>>>>>>>>>>>>>>>>>> at Module._compile (module.js:374:25)
>>>>>>>>>>>>>>>>>>>> at Object.Module._extensions..js (module.js:417:10)
>>>>>>>>>>>>>>>>>>>> at Module.load (module.js:344:32)
>>>>>>>>>>>>>>>>>>>> at Function.Module._load (module.js:301:12)
>>>>>>>>>>>>>>>>>>>> at Function.Module.runMain (module.js:442:10)
>>>>>>>>>>>>>>>>>>>> at startup (node.js:136:18)
>>>>>>>>>>>>>>>>>>>> at node.js:966:3
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> npm ERR! Linux 4.15.0-55-generic
>>>>>>>>>>>>>>>>>>>> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run"
>>>>>>>>>>>>>>>>>>>> "compile"
>>>>>>>>>>>>>>>>>>>> npm ERR! node v4.2.6
>>>>>>>>>>>>>>>>>>>> npm ERR! npm v3.5.2
>>>>>>>>>>>>>>>>>>>> npm ERR! code ELIFECYCLE
>>>>>>>>>>>>>>>>>>>> npm ERR! loris at 1.0.0 compile: `webpack`
>>>>>>>>>>>>>>>>>>>> npm ERR! Exit status 1
>>>>>>>>>>>>>>>>>>>> npm ERR!
>>>>>>>>>>>>>>>>>>>> npm ERR! Failed at the loris at 1.0.0 compile script
>>>>>>>>>>>>>>>>>>>> 'webpack'.
>>>>>>>>>>>>>>>>>>>> npm ERR! Make sure you have the latest version of
>>>>>>>>>>>>>>>>>>>> node.js and npm installed.
>>>>>>>>>>>>>>>>>>>> npm ERR! If you do, this is most likely a problem with
>>>>>>>>>>>>>>>>>>>> the loris package,
>>>>>>>>>>>>>>>>>>>> npm ERR! not with npm itself.
>>>>>>>>>>>>>>>>>>>> npm ERR! Tell the author that this fails on your system:
>>>>>>>>>>>>>>>>>>>> npm ERR! webpack
>>>>>>>>>>>>>>>>>>>> npm ERR! You can get information on how to open an
>>>>>>>>>>>>>>>>>>>> issue for this project with:
>>>>>>>>>>>>>>>>>>>> npm ERR! npm bugs loris
>>>>>>>>>>>>>>>>>>>> npm ERR! Or if that isn't available, you can get their
>>>>>>>>>>>>>>>>>>>> info via:
>>>>>>>>>>>>>>>>>>>> npm ERR! npm owner ls loris
>>>>>>>>>>>>>>>>>>>> npm ERR! There is likely additional logging output
>>>>>>>>>>>>>>>>>>>> above.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> npm ERR! Please include the following file with any
>>>>>>>>>>>>>>>>>>>> support request:
>>>>>>>>>>>>>>>>>>>> npm ERR! /var/www/loris/npm-debug.log
>>>>>>>>>>>>>>>>>>>> Makefile:14: recipe for target 'javascript' failed
>>>>>>>>>>>>>>>>>>>> make: *** [javascript] Error 1
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 7 Αυγ 2019 στις 5:41 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks, have you tried all of these steps?
>>>>>>>>>>>>>>>>>>>>> - clear your browser cache (and refresh a few times)
>>>>>>>>>>>>>>>>>>>>> - delete any files in your smarty/templates_c
>>>>>>>>>>>>>>>>>>>>> directory (this will clear the template cache - do Not touch
>>>>>>>>>>>>>>>>>>>>> smarty/templates/)
>>>>>>>>>>>>>>>>>>>>> - run `make` (per the 21 release notes, this replaces
>>>>>>>>>>>>>>>>>>>>> the composer commands used in previous releases to update your dependencies)
>>>>>>>>>>>>>>>>>>>>> - restart apache (doesn't hurt)
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Let us know how it goes -- let us know what difference
>>>>>>>>>>>>>>>>>>>>> you see after, with your logs. A
>>>>>>>>>>>>>>>>>>>>> lso please send us your Config path settings (see these
>>>>>>>>>>>>>>>>>>>>> Troubleshooting Queries
>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>)
>>>>>>>>>>>>>>>>>>>>> if you're still seeing front-end issues.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo cat
>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/error.log
>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422501 2019]
>>>>>>>>>>>>>>>>>>>>>> [mpm_prefork:notice] [pid 1267] AH00163: Apache/2.4.18 (Ubuntu)
>>>>>>>>>>>>>>>>>>>>>> OpenSSL/1.0.2g configured -- resuming normal operations
>>>>>>>>>>>>>>>>>>>>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid
>>>>>>>>>>>>>>>>>>>>>> 1267] AH00094: Command line: '/usr/sbin/apache2'
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> And as for the access.log the content are empty
>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l
>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>>>>>> -rw-r----- 1 root adm 0 Ιούν 28 14:09
>>>>>>>>>>>>>>>>>>>>>> /var/log/apache2/access.log
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Also i noticed a loris_access.log.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> The only non-blank pages are:
>>>>>>>>>>>>>>>>>>>>>> mri_violations, dataquery does not exist at all,
>>>>>>>>>>>>>>>>>>>>>> statistics, data_team_helper, genomic_browser, configuration and
>>>>>>>>>>>>>>>>>>>>>> server_processes_manager/ prints "Required configuration settings for
>>>>>>>>>>>>>>>>>>>>>> Server Processes Manager are missing. Cannot continue."
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 6 Αυγ 2019 στις 10:13 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios and LORIS community --
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> When upgrading to brand-new release 21 -- just a
>>>>>>>>>>>>>>>>>>>>>>> reminder to follow the release notes and run the new
>>>>>>>>>>>>>>>>>>>>>>> *make* file to update your dependencies (instead of
>>>>>>>>>>>>>>>>>>>>>>> using *composer* commands).
>>>>>>>>>>>>>>>>>>>>>>> We've also updated the Wiki page
>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Updating-your-LORIS>
>>>>>>>>>>>>>>>>>>>>>>> to clarify that the release notes for each version will tell you what to
>>>>>>>>>>>>>>>>>>>>>>> run.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> If your current version is not the last release
>>>>>>>>>>>>>>>>>>>>>>> (20.3), it's still important to upgrade to each minor release increment
>>>>>>>>>>>>>>>>>>>>>>> (e.g. 20.2, 20.3) before making the leap to 21.0.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> If you're getting blank pages, post-upgrade -- Try
>>>>>>>>>>>>>>>>>>>>>>> clearing your cache.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Got questions or feedback e.g. on the Release Notes?
>>>>>>>>>>>>>>>>>>>>>>> please don't hesitate to let us know.
>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers,
>>>>>>>>>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>> Could you also let us know -- on which pages is
>>>>>>>>>>>>>>>>>>>>>>>> content visible, and on which pages/modules is content not visible for you?
>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers,
>>>>>>>>>>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thanks Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>> That's good to know. It sounds like you've
>>>>>>>>>>>>>>>>>>>>>>>>> checked that your /var/www/loris/project/config.xml file get populated
>>>>>>>>>>>>>>>>>>>>>>>>> properly.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Please send us the last few errors you're seeing
>>>>>>>>>>>>>>>>>>>>>>>>> in your apache error log file, and your config paths and we can see what's
>>>>>>>>>>>>>>>>>>>>>>>>> happening with your front end --
>>>>>>>>>>>>>>>>>>>>>>>>> Run these Troubleshooting Queries
>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>>>>>>>>>>>>>>>>>>>>>>>>> to get your config path settings, given your front end is not displaying
>>>>>>>>>>>>>>>>>>>>>>>>> fully.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> The Loris-MRI repo
>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21
>>>>>>>>>>>>>>>>>>>>>>>>> install/upgrade would then be your next steps.
>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> I am using a VM. What i did was:
>>>>>>>>>>>>>>>>>>>>>>>>>> 1) Download the files from
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris and replace them
>>>>>>>>>>>>>>>>>>>>>>>>>> to my existing /vaw/www/loris folder.
>>>>>>>>>>>>>>>>>>>>>>>>>> 2) Execute the composer install --no-dev and
>>>>>>>>>>>>>>>>>>>>>>>>>> then composer dump-autoload as mentioned here
>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Execute install.sh from /var/www/loris/tools
>>>>>>>>>>>>>>>>>>>>>>>>>> and because LORIS already existed i moved a .config file, then re-executed
>>>>>>>>>>>>>>>>>>>>>>>>>> the install.sh successfully
>>>>>>>>>>>>>>>>>>>>>>>>>> 4 ) As for the database, i dropped the schema and
>>>>>>>>>>>>>>>>>>>>>>>>>> i executed the installdb.php
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotorios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks - when you re-installed did you start on
>>>>>>>>>>>>>>>>>>>>>>>>>>> a fresh root path / VM or might some of your old system setting still
>>>>>>>>>>>>>>>>>>>>>>>>>>> apply?
>>>>>>>>>>>>>>>>>>>>>>>>>>> (And if you did any steps similar to an upgrade,
>>>>>>>>>>>>>>>>>>>>>>>>>>> did you follow the Upgrade steps in the Release Notes, from both repos?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> About the TR_range column - it was recently
>>>>>>>>>>>>>>>>>>>>>>>>>>> split (MRI pr339
>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/pull/339>) split
>>>>>>>>>>>>>>>>>>>>>>>>>>> into TR_min and _max columns. Given the code was trying to query TR_range
>>>>>>>>>>>>>>>>>>>>>>>>>>> which does not exist in your mri_protocol table, double-check which version
>>>>>>>>>>>>>>>>>>>>>>>>>>> of the Loris repo (tables) and the Loris-MRI repo (code) you have installed
>>>>>>>>>>>>>>>>>>>>>>>>>>> to ensure they match.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I reinstalled LORIS to 21 version and now the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> content is not visible at all at most pages.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> query mri_protocol which doesn't have TR_range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'where clause' at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> without execute() at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $count_mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in numeric gt (>) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'TR_range' in 'field list' at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> First, just a note: we've released LORIS 21
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this week with some major new features and cleanup -- especially if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> early in your setup phase, check out the Release notes for both the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/releases/tag/v21.0.0>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repos.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your screenshots -- your empty
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table should be at the root of these issues :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The mri_protocol table must be populated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified or matched to scan types in this table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> By default, this table is populated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries for t1, t2, fMRI and DTI (Insert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements for 21 release branch are here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Feel free to restore our default records and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> broaden their parameters to match all your scan types.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re Defaced, native, selected -- these filter
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scans displayed as you move to the next page (View Session), instead of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> viewing "all types" of scans from a given session :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "defaced" means that a defacing script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "native" means that no pre-processing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has been performed on the scan (it's raw data),
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - "selected" will show only volumes that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have been QC'd and "selected" as the best of their type -- used to display
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> only the best quality T1 image instead of all T1s acquired in a session,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> e.g.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re QC Comments --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Once you have successfully loaded scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (matched to the mri_protocol table), you'll be able to use the Imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Browser's View Session subpage to enter/view QC comments on each volume, or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for each visit.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> These are stored directly in the database,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and linked to each scan. (Table name:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Visit-level QC comments are linked to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a walkthrough of the Imaging setup -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> please see the Imaging Setup guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An old LORIS walkthrough video
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://www.youtube.com/watch?v=HDWC6RUbI6A> can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through some of the Imaging front-end features, starting at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 8:00
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS' imaging modules have been updated many
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> times since this video, but the functionality and workflow is similar.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know how it goes once you have entries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your mri_protocol table -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the candidate_list page i can see this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i press the link under PSCID i get to see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and if i press the link under Scan Done it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redirects me to imaging_browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the mri_violations page i also see No
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> results ( neither on resolved / not resolved ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the imaging_uploader i can see the record
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If i click on the tarchive info i get to see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the Protocol Name which i think is the acquisition we wanted?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also my mri_protocol table is empty.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Furthermore i would like to ask about the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> defaced, native, selected. What exactly is native and selected? And where
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are the qc comments stored?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally a walkthrough would be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Glad to hear you're making progress with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit labels. To follow up on your last few emails:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert statements for the Visit Windows table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> As Cecile mentioned, the consistency of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label format is important: V01, v01, V1, 01 -- whichever you select
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to use is fine; we use V01 by default across all documentation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b- For Password reset, there is a script in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the tools/ directory so that a back-end administrator can reset any
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end user password, including Admin. (See info on setting up /
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resetting User passwords in the Wiki's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Setup Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c- The minc file not being registered --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This means the SeriesDescription
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (Acquisition Protocol) in you Dicom header was not matched to any scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> listed in the mri_protocol database table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted").
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The MRI Violations module (Readme here)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/tree/minor/modules/mri_violations>will show
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you the details of this mismatch --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Go to the module (under the Imaging menu),
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find your scan and click the link "Could not identify scan type" -- in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next subpage you can compare the scan's actual parameters against the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table values or perhaps ensure your DICOMs are labelled consistently.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know if this works for you -- we can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also walk you through an example of non-identified scans on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Demo.loris.ca (MRI Violations module).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I hope this is sufficient as the error for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label disappeared.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Please see the attached file. Also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something i found.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> since the AcquisitionProtocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> known hash and by deleting the rows from the login_history i was able to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> login.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there was no visit label 01 in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and i don't know how to insert it because the record
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> requires lots of attributes. Also the system for a reason asked me to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update my password and now i don't remember it and my account got
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> suspended. Is there a way to reset it or set a simple password? I updated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the password hash in the users table by using the hash from another LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> setup we had and i still couldn't login ( also the attribute password is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> always NULL and the expiration date is 1999-01-01 for some reason ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the Visit_Windows table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, I noticed that in a previous
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dataset, the label was V1. Does that refer to the same visit? If so, you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might want to harmonize the visit labels so they are all the same across
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> datasets for a given timepoint, meaning you will need to relabel scans when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label is different but referring to the same visit label (v01 =
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V1 etc...).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you had suggested but it appears that this problem hasn't been resolved
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yet.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --> using user-defined
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> filterParameters for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid. Logging to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with reason Visit label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion of mincs fails. Please see the output.txt file i attached. Also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is there something else i need to change at the paths configuration?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We are making progress!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> from the fact that your psc table does not have the MRI_alias populated for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCC site. Running the following query in the mysql database should fix
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alias="DCC" WHERE Name="Data Coordinating Center";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (make sure to change the Aliases between sites, they should all be unique).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let me know how it goes!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I did the modifications you suggested, i still get the "no mincs inserted"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error, now i am getting the "No center found this candidate" error ( how do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i fix that? from what i see the .dcm files contains a 'Institution Name',
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is that the center? ), so i guess that's why the validation fails, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed the force variable of tarchiveLoader to 1, shouldn't it have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted the mincs then? Also it is optional to have a mail server, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ( from what i see the mail error does not affect the $valid_study, so i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assume we are okay with that )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you a lot,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you just need to update a few config settings from the frontend in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config module (under the Admin menu).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.31.35 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the config module and update the "LORIS-MRI code" config setting to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri (my guess is that currently, it is set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data) and click on the submit button.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.32.50 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the Configuration module and update the "Loris-MRI Data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" to /data/loris/data/ (my guess is that it is empty at the moment
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in your database which is why $data_dir is not defined when you run the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10.40.52 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> environment file and it might be a good idea to update your PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable to the following (it has been added to the code a few releases ago
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as we realized this was needed for the libraries. Not sure which version of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LORIS-MRI you are using but it does not hurt to update this variable to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I suggest below):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> export
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> experiencing so much trouble setting things up. We probably need to update
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> our WIKI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be in the environment file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> π.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/. Somewhere I might have messed something up but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remember following the instructions in the wiki.For example when i tried to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> execute the batch_uploads_imageuploader perl script the line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my $command =
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "$bin_dir/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for example: it was repeating a pattern and had LORIS instead of loris ( i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> think the mistake was that in the wiki it suggested to use $PROJECT for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the name of the folder and i choosed 'loris'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Config setting not set (based on the first error message you got when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> running it the first time). You need to set a value for "Loris-MRI Data
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Directory" in the Config module under the Imaging pipeline section (from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> what I can see, it would be /data/loris/data/ for your setup).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> message the second time is that the pipeline checks if the DICOM study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted in the tarchive table. Since you ran the study once
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already, the study is inserted into the tarchive, hence the message.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, the pipeline did not complete as the MINC files were not created
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and inserted into the files/parameter_file table. In order to continue the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion, you will then need to run the tarchiveLoader command suggested
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in the terminal during the second run:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your setup. Where are the scripts located? In /data/loris/bin/mri or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Paths section was set to "/data/LORIS/data" but it should have been set to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the directory where the scripts are located (most probably
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in pattern match (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> source
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 219.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 721.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $data_dir in concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> still the Mincs are not inserted and i am getting this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has already been run with tarchiveID: 7.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion pipeline, please run tarchiveLoader from a terminal as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thought that deleting the files from the tarchive was enough. And i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> executed the last proposed command to continue to rest of the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline ( check the image ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:05 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Every visits of candidates are created in the session table with one entry
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> per CandID/VisitLabel. So if the imaging pipeline created visits in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> session table (that are not attached to instruments) and you want to clean
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your database completely, you can delete entries in that table as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging pipeline can create the visit in the session table as long as the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label is present in the Visit_Windows table (which means the visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label stored in the PatientName is a valid visit label).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> populating the Visit_Windows table and set the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of badly labelled MRI data that are complex to relabel.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate creation, if you execute the following steps, the pipeline should
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be able to create candidates:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> section of the config module the config setting "Upload creation of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates" to Yes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to the LORIS server instead of uploading it via the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as you did until now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> replaced the name of the patient in the .dcm files and now i am getting an
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error that the visit label does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be automatically created.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will be considered for inserting into the database: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file is /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3:38 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the session table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> non-phantom file like this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> N DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error in the log.txt file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> command: /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DICOM header does not start with DCC0000_258024_V1 from the mri_upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> repeated for each .dcm file. Should i preprocess every .dcm file and change
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName to "DCC0000_258024_V1"?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate profile i have to create a new one each time before i try to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a file? Is there already a way to create a candidate profile and get
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the DCCID and PSCID without the user interface?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 5:00 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom with a blank studyUID, maybe someone accidentally removed it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> must have been done to the DICOM files. I have never seen a study with no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID out of the scanner. Usually, you need to manually erase it with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some tool. However, DICOMs never cease to surprise me...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> remove all of my patients and uploads?: because i want to try to reupload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> all the testing dicoms we had with a clean database.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will offer a script to remove all the entries and files specific to an
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload. However, this release is not yet out. Hopefully in the next few
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> weeks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your case is particular and that you just want to start with a clean
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database, the following deletes should work (hopefully I won't forget any
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_violations_log;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol_violated_scans;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRICandidateErrors;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files_qcstatus; # (if you played with the QC part of the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feedback_mri_comments; # (if you played with the QC part of the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_series;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where PSCID="scanner";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to also delete entries in the session and candidate table too?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the profile of a patient ( are the patients stored in the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table? because i can't see the ghosts ), because will it automatically be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created when importing a dicom?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> fully this question. All candidates are stored in the candidate table. The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom scans however are attached to a scanner candidate depending on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> where the scan happened. It is a bit of a weird concept that we have to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> redesign eventually but never got a chance to get to it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your question, otherwise, don't hesitate to let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between uploading a dicom as phantom instead of importing as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IDs and visit label are valid at the time of upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> phantom, it expects that the DICOM field PatientName and uploaded filename
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contains the string "phantom". We enforced this behaviour on the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploader side in recent releases but I can't remember which one. Probably
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the upcoming 21.0 release.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> might seem cumbersome but they are here to ensure that the files inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> are all valid and labelled properly as it is a bit messy to have to delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files that were wrongly labelled. At least, the delete script present in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release 21.0 will make this process easier but it is still good practice to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> verify those things.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the answers to your questions will be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> list: you will find the initial answer I gave Sotirios below. I forgot to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cc the loris-dev in my earlier reply...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> στις 12:02 π.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out. Since your email was already organized in points, I will reply
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directly below your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the StudyUID is blank on the header?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> field used in our pipeline at the moment to check whether a DICOM study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> already inserted into LORIS with that same StudyUID since it is supposed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be unique for every single study. Currently, we do not support insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM studies if they do not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason why the StudyUID is blank in the DICOM headers in your DICOM files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Did they go through some processes before upload to LORIS?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload a non-phanton case i need a 'Visit Label'. Is there already a script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can create a new visit label for a specific Candidate, so i can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provide it as input afterwards to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-end allows for it but if you use batch_uploads_imageuploader, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion scripts could create the visit label for you. However, it does
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> need to be included in the patient name in order for the script to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which label it should use.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the insertion scripts will create a V02 visit for MTL0123 if the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName field for the dataset is MTL0123_456789_V02 with Stage marked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> as "Not Started".
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the script to create the visit for the candidate, you have to make sure
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that all the visit label of your projects were inserted in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Most of the time, the MINC files that failed insertion into the imaging
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> browser end up in the MRI violation module where you can see what went
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrong with the acquisitions not inserted. If you notice that the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> should be inserted as a specific protocol, you can force the insertion as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in section 4.3.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> feeling that you want to be able to insert MINC files that did not go
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through the whole pipeline insertion (DICOM archival, then dcm2mnc, then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> protocol identification, then insertion...). In theory, you could call
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any MINC file, provided you have at least the following information:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the MINC files or DICOM archive path from which those MINC files were
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script will do the subject information and protocol validation etc...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> come from the same uploadID or TarchiveID, then you could run a loop in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> bash calling the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script like this for files deriving from uploadID=1:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | while read f; do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod -uploadID 1 -mincPath $f; done
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Shen Wang
>>>>>>>>>>>>> Loris <https://github.com/aces/Loris> Developer
>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>> McGill University
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Shen Wang
>>>>>>>>> Loris <https://github.com/aces/Loris> Developer
>>>>>>>>> Montreal Neurological Institute
>>>>>>>>> McGill University
>>>>>>>>>
>>>>>>>>> --
>>>>>>>> Shen Wang
>>>>>>>> Loris <https://github.com/aces/Loris> Developer
>>>>>>>> Montreal Neurological Institute
>>>>>>>> McGill University
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Loris-dev mailing list
>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> christine.rogers at mcgill.ca
>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>> Montreal Neurological Institute
>>>>>>> McGill University | Montreal | Canada
>>>>>>>
>>>>>>
>>>>
>>>> --
>>>> Shen Wang
>>>> Loris <https://github.com/aces/Loris> Developer
>>>> Montreal Neurological Institute
>>>> McGill University
>>>>
>>>>
>>
>> --
>> Shen Wang
>> Loris <https://github.com/aces/Loris> Developer
>> Montreal Neurological Institute
>> McGill University
>>
>>
--
Shen Wang
Loris <https://github.com/aces/Loris> Developer
Montreal Neurological Institute
McGill University
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