[Loris-dev] Upgrading to Loris 21 - new make file
John Saigle
john.saigle at mcin.ca
Tue Aug 13 16:52:10 EDT 2019
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
>
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