[Loris-dev] Upgrading to Loris 21 - new make file
Shen Wang
wangshen.mcin at gmail.com
Tue Aug 13 21:21:40 EDT 2019
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
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