[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Oct 1 09:33:15 EDT 2019
When mincs are inserted their corresponding rows at the file table are
inserted too
[image: image.png]
i would like to insert their rows at file_qcstatus as well, because i don't
want manually to label them as passed throught the interface
[image: image.png]
That is the trigger i wrote
CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER
INSERT ON `files` FOR EACH ROW
BEGIN
INSERT INTO files_qcstatus
SET FileID = NEW.FileID,
SeriesUID = NEW.SeriesUID,
EchoTime = NEW.EchoTime,
QCStatus = "Pass",
QCFirstChangeTime = NOW(),
QCLastChangeTime = NOW();
END
although it contains some errors
DBD::mysql::db do failed: Out of range value for column 'QCFirstChangeTime'
at row 1 at
/data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key
constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
`FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`))
at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
Στις Τρί, 1 Οκτ 2019 στις 4:21 μ.μ., ο/η Cecile Madjar <
cecile.madjar at mcin.ca> έγραψε:
> Hi Sotirios,
>
> In the mri_upload table, there is a TarchiveID column associated with the
> MRI upload you inserted. When this value is NULL, it means no DICOMs were
> inserted into the tarchive tables. At the end of the insertion of the
> DICOMs in the tarchive tables, this value is updated with the correct
> TarchiveID associated with the upload.
>
> Could this correspond to what you want to do?
>
> Regarding the files_qcstatus, this table is only linked to the files table
> (hence, the MINC files). You could always create a new table for
> dicom_qcstatus and link it to the tarchive table?
>
> Cécile
>
> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi,
>>
>> i would like whenever a dicom is imported to mark all their coressponding
>> qc_status to "pass". I was thinking of creating a trigger for that, but
>> which tables do i need to add entries to? So far from what i see i need to
>> add entres at the table "files" whenever an insertion happens to
>> files_qcstatus.
>>
>> Thanks
>>
>> Στις Δευ, 30 Σεπ 2019 στις 4:04 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> έγραψε:
>>
>>> Oh, sorry i should have asked for StudyID, at the beginning of my email
>>> i sent 3 hours ago (not StudyUID).
>>>
>>> Στις Δευ, 30 Σεπ 2019 στις 3:55 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>>> Hi,
>>>>
>>>> that's the Study Instance UID, not the StudyID. So the StudyID i am
>>>> looking for is not stored in the database?
>>>>
>>>> [image: image.png]
>>>>
>>>> Thanks.
>>>>
>>>> Στις Δευ, 30 Σεπ 2019 στις 3:38 μ.μ., ο/η Cecile Madjar <
>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> The StudyUID is stored in the DicomArchiveID field of the
>>>>> tarchive table. It can also be found in the metadata field but it is mixed
>>>>> with many other information.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> Cécile
>>>>>
>>>>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Is StudyUID stored somewhere at the tables? At the tarchive table,
>>>>>> specifically at the AcquisitonMetadata column i found something called
>>>>>> 'Unique Study ID" in its context, but that must be the Study Instance UID.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Στις Παρ, 27 Σεπ 2019 στις 4:22 μ.μ., ο/η Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> Your observation is correct. A little explanation below.
>>>>>>>
>>>>>>> MINC files get inserted into the MRI violation tables if:
>>>>>>>
>>>>>>> - the scan type could not be identified (not matching an entry
>>>>>>> in the mri_protocol table)
>>>>>>> - one parameter of the scan type is out of the expected range
>>>>>>> present in the mri_protocol_checks (extra filtering in case you need to be
>>>>>>> stricker on some parameters not present in the mri_protocol table)
>>>>>>> - if the CandID and PSCID do not match
>>>>>>>
>>>>>>> The following cases do not get in the MRI violation tables as it
>>>>>>> happens before the conversion of the DICOM to MINC files and only MINC
>>>>>>> files violations are logged there:
>>>>>>>
>>>>>>> - "No single DICOM" (since no valid DICOM could be found to
>>>>>>> convert to MINC)
>>>>>>> - "Study already inserted" (duplicate StudyUID) since this error
>>>>>>> happens at the dicomTar.pl level (way before conversion into MINC files)
>>>>>>>
>>>>>>> Glad everything is working out!!
>>>>>>> Best,
>>>>>>>
>>>>>>> Cécile
>>>>>>>
>>>>>>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> the mri passed, for some reason it consumed 5.12GB of ram. Now
>>>>>>>> about the mri_violations, dicoms are triggered to be inserted there only if
>>>>>>>> there is a violation for Tr_min, Tr_max, in general for its header
>>>>>>>> parameter? Because i don't see the cases of 'No single dicom" or with the 2
>>>>>>>> studyiuid to be there.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Στις Πέμ, 26 Σεπ 2019 στις 5:07 μ.μ., ο/η Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Sorry to hear you are having issues with the memory. I think most
>>>>>>>>> of our VMs are set up with 4GB of RAM so with 4GB you should be fine.
>>>>>>>>>
>>>>>>>>> Hope this helps!
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>>
>>>>>>>>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> about that dicom that had that insertion error it's about 30mb
>>>>>>>>>> and when it is being processed the ram is being drastically increased from
>>>>>>>>>> 2gb to 3.28 and then the whole virtual machine is frozen. What is the
>>>>>>>>>> recommended size of ram for using Loris?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 24 Σεπ 2019 στις 11:24 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>
>>>>>>>>>>> For the delete script issue, if you are absolutely certain that
>>>>>>>>>>> no processes are run for that uploadID, you can update the mri_upload table
>>>>>>>>>>> and set the column Inserting to 0 instead of 1 for that
>>>>>>>>>>> uploadID. It looks like for some reason the scripts did not update this
>>>>>>>>>>> field when it stopped the insertion. Not sure why that would be the case
>>>>>>>>>>> though.
>>>>>>>>>>> Note: only do that update if you are certain that there is no
>>>>>>>>>>> processing happening.
>>>>>>>>>>>
>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> about the Dicoms i reported that didn't have a StudyID they
>>>>>>>>>>>> actually do
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> I thought that this might be a permission because "w" was
>>>>>>>>>>>> missing at the group. After using chmod -R 775 only 102809579 passed, but
>>>>>>>>>>>> with no mnic files. Also now i have this error
>>>>>>>>>>>>
>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$
>>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>> Cannot delete upload 34: the MRI pipeline is currently
>>>>>>>>>>>> processing it.
>>>>>>>>>>>>
>>>>>>>>>>>> How can solve this?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τρί, 24 Σεπ 2019 στις 2:30 π.μ., ο/η Sotirios
>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>
>>>>>>>>>>>>> To give you a brief idea:
>>>>>>>>>>>>> Per folder it will:
>>>>>>>>>>>>> 1) Delete all the .bak files
>>>>>>>>>>>>> 2) Locate .dcm files and update the Patient header
>>>>>>>>>>>>> 3) Furthermore we are interesting in finding TR_min, TR_max,
>>>>>>>>>>>>> TE_min, TE_max parameters of T1 protocol and do an update at the
>>>>>>>>>>>>> mri_protocol table
>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>> For some reason some files are missing
>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>
>>>>>>>>>>>>> In total i have 7 folders
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> 3/7 passed
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> Also about the first patient with DC0000 had a violation "T1
>>>>>>>>>>>>> AXIAL SE GADO", but my script didn't output a TE of 17 nowhere and i find
>>>>>>>>>>>>> that weird since Loris detects the SeriesDescription.
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>
>>>>>>>>>>>>> 102327840 and 102809579 outputs "The target directory does not
>>>>>>>>>>>>> contain a single DICOM file.", therefore they are missing their StudyUID
>>>>>>>>>>>>>
>>>>>>>>>>>>> 102506134 has 2 studyuid "You can't use it with data from
>>>>>>>>>>>>> multiple studies."
>>>>>>>>>>>>>
>>>>>>>>>>>>> and 102761034 "No data could be converted into valid MINC
>>>>>>>>>>>>> files. localizer, scout will not be considered!" What is this?
>>>>>>>>>>>>>
>>>>>>>>>>>>> If i wanted to force the insertion of 102327840, 102809579 and
>>>>>>>>>>>>> 102506134 can i just pass a flag parameter to
>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or modify
>>>>>>>>>>>>> imaging_upload_file.pl?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>> PS
>>>>>>>>>>>>>
>>>>>>>>>>>>> To diagnose a folder search the name of the folder at
>>>>>>>>>>>>> dicom_output.txt.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 4:54 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>> Glad to hear about your progress.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Yes, the script you used to delete imaging data is fully
>>>>>>>>>>>>>> documented here
>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md>
>>>>>>>>>>>>>> -- let us know if you didn't find the answers you were looking for there.
>>>>>>>>>>>>>> (Is it possible the null row in *mri_scanner* seen in your
>>>>>>>>>>>>>> database management software is a visual placeholder for you as the user?
>>>>>>>>>>>>>> I'm not sure why a scanner would ever be registered with ID='0' as your
>>>>>>>>>>>>>> screenshot showed.)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I fixed it with this
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 4:37 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I tried to create a new candidate using the API, is there
>>>>>>>>>>>>>>>> something wrong with the structure? why did i receive a 500 internal error?
>>>>>>>>>>>>>>>> In the loris-error log it state that there is something wrong with token,
>>>>>>>>>>>>>>>> but i verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535]
>>>>>>>>>>>>>>>> [client 127.0.0.1:59674] PHP Fatal error: Uncaught
>>>>>>>>>>>>>>>> TypeError: Argument 1 passed to SinglePointLogin::JWTAuthenticate() must be
>>>>>>>>>>>>>>>> of the type string, null given, called in
>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>> defined in
>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in
>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Is there a way also to delete candidates? Just to let you
>>>>>>>>>>>>>>>>> know what i did to clear candidates, because maybe i may have missed
>>>>>>>>>>>>>>>>> dependencies.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> First i deleted all their uploads
>>>>>>>>>>>>>>>>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a
>>>>>>>>>>>>>>>>> way to omit the backup file ? )
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Afterwards i had some scanner candidates, so i deleted all
>>>>>>>>>>>>>>>>> the entries from mri_scanner except that i couldn't delete this entry with
>>>>>>>>>>>>>>>>> the 0 ID.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Lastly i deleted the session and then the candidate table.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> We recommend that you use our existing tools for creating
>>>>>>>>>>>>>>>>>> new candidates - either the LORIS API or if you are using a PHP script, by
>>>>>>>>>>>>>>>>>> calling the Candidate class's createNew()
>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200>function.
>>>>>>>>>>>>>>>>>> These will create the necessary records for you. (It's not recommended to
>>>>>>>>>>>>>>>>>> make direct modifications to mysql database tables in your script, if I
>>>>>>>>>>>>>>>>>> understand you.)
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The CandID should be a randomized 6 digit randomized ID,
>>>>>>>>>>>>>>>>>> and there are multiple reasons for this.
>>>>>>>>>>>>>>>>>> You can use the PSCID for project-specific IDs and the
>>>>>>>>>>>>>>>>>> External ID field in the candidate table can also be used for any values
>>>>>>>>>>>>>>>>>> you like.
>>>>>>>>>>>>>>>>>> Additionally, any number of custom IDs can be added in
>>>>>>>>>>>>>>>>>> parallel - these are entered/visible in the Candidate Information module
>>>>>>>>>>>>>>>>>> and added in the back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> We are building a script that will auto insert the
>>>>>>>>>>>>>>>>>>> candidates based on their ExternalID. We would like to know whethere when
>>>>>>>>>>>>>>>>>>> we are creating a new profile in the candidate table, if we also have to
>>>>>>>>>>>>>>>>>>> insert a new record at another table? Furthermore is there a problem that
>>>>>>>>>>>>>>>>>>> in our case CandID won't be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie
>>>>>>>>>>>>>>>>>>> Legault, Mrs <melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> That would normally be the case but the numeric part of
>>>>>>>>>>>>>>>>>>>> the PSCID get paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Ex. for sequential ID made of center ID of `ABC` plus 4
>>>>>>>>>>>>>>>>>>>> numerical char with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ABC0001
>>>>>>>>>>>>>>>>>>>> ABC0002
>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>> ABC0010
>>>>>>>>>>>>>>>>>>>> ...
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> thus sorting them ascending will always get the latest
>>>>>>>>>>>>>>>>>>>> value generated as the max value.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Mélanie
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I see, although the PSCID value is varchar(255), it
>>>>>>>>>>>>>>>>>>>> must be stored within a specific length of characters. Otherwise if we were
>>>>>>>>>>>>>>>>>>>> to sort strings with different lengths the result would not be sorted
>>>>>>>>>>>>>>>>>>>> correctly ( e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie
>>>>>>>>>>>>>>>>>>>> Legault, Mrs <melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>>>> The code simply look for the PSCID with the max value
>>>>>>>>>>>>>>>>>>>> and increase that value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Mélanie Legault | Software developer | Faculty of
>>>>>>>>>>>>>>>>>>>> Medicine | McGill University
>>>>>>>>>>>>>>>>>>>> 3801 University, Montréal, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> how does Loris determine the next available PSCID value
>>>>>>>>>>>>>>>>>>>> for a new candidate?
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>> e.x in the default case the PSCID is sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> the parameters in the mri_protocol you have assigned
>>>>>>>>>>>>>>>>>>>> are global standard? or were assigned after trial and error?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Given you have done the initial setup of your tables to
>>>>>>>>>>>>>>>>>>>> match your intended protocol/parameters according to instructions --
>>>>>>>>>>>>>>>>>>>> the Troubleshooting guide documentation recommends
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes>
>>>>>>>>>>>>>>>>>>>> re-running the pipeline (and first deleting prior uploads).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> *if i were to change their status to resolve what would
>>>>>>>>>>>>>>>>>>>> happen?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I noticed that i can view the mnics at the brainbrowser
>>>>>>>>>>>>>>>>>>>> from the mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/ if i were to click their issue to resolve what
>>>>>>>>>>>>>>>>>>>> would happend? would they appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The defaut values of the schema exists in my local
>>>>>>>>>>>>>>>>>>>> database. If i adjust the default values of TR_min and TE_min the mincs
>>>>>>>>>>>>>>>>>>>> will be uploaded?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>>>> mri_protocol table ? (and mri_scan_type table too, for additional types
>>>>>>>>>>>>>>>>>>>> of scans)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Like the psc table, this is a pre-requisite for the
>>>>>>>>>>>>>>>>>>>> Imaging insertion setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> To add new rows, just use MySQL insert statements. You
>>>>>>>>>>>>>>>>>>>> can adapt the insert statements which load the default table values -->
>>>>>>>>>>>>>>>>>>>> e.g. Here on GitHub :
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I see that i can edit the values but not how to insert
>>>>>>>>>>>>>>>>>>>> new rows.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> If i choose Inserted with flag then will the minc be
>>>>>>>>>>>>>>>>>>>> inserted?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> For the MRI Violations module, the screenshot is
>>>>>>>>>>>>>>>>>>>> enough.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> It says "could not identify scan type", which we knew
>>>>>>>>>>>>>>>>>>>> already. Did you click on the link on those words?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> It will take you to the next page of the module,
>>>>>>>>>>>>>>>>>>>> showing for each scan what the scan parameters were, and will also show for
>>>>>>>>>>>>>>>>>>>> comparison what's stored in your *mri_protocol*
>>>>>>>>>>>>>>>>>>>> table.
>>>>>>>>>>>>>>>>>>>> Compare these values to find which parameter was not
>>>>>>>>>>>>>>>>>>>> correct according to your *mri_protocol* table scan
>>>>>>>>>>>>>>>>>>>> type definitions.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> You may end up broadening your mri_protocol value
>>>>>>>>>>>>>>>>>>>> ranges (e.g. TR, TE) for scans.
>>>>>>>>>>>>>>>>>>>> This can be done in the front-end, by editing the
>>>>>>>>>>>>>>>>>>>> database table directly in the same subpage of the MRI Violations module.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The MRI Violations module features are explained in
>>>>>>>>>>>>>>>>>>>> more detail in the Help text for this module inside LORIS (click the
>>>>>>>>>>>>>>>>>>>> ["?"] icon in the menu bar.)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md>
>>>>>>>>>>>>>>>>>>>> : no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> looks like my previous email's attachment wasn't
>>>>>>>>>>>>>>>>>>>> delivered due to security reasons, i uploaded my file at google drive
>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> From Dicat's view seems that dcmodify worked in both
>>>>>>>>>>>>>>>>>>>> cases
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> For the mri_violations i attached the .html output from
>>>>>>>>>>>>>>>>>>>> webbrowser, so that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> About the dcmodify command -- I'm not sure why you're
>>>>>>>>>>>>>>>>>>>> getting an Endian warning. (it's a warning not an error, correct?)
>>>>>>>>>>>>>>>>>>>> To clarify -- Were the DICOM headers (PatientName) all
>>>>>>>>>>>>>>>>>>>> successfully relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to verify and/or update
>>>>>>>>>>>>>>>>>>>> local DICOM headers -- though your dcmodify command is a great and fast
>>>>>>>>>>>>>>>>>>>> solution for bulk header updates.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> If you're concerned about fields being changed (e.g.
>>>>>>>>>>>>>>>>>>>> "(2001,105f)" from the warning message) - you can also dcmdump a DICOM
>>>>>>>>>>>>>>>>>>>> slice before and look at these fields specifically.
>>>>>>>>>>>>>>>>>>>> It's also not a bad "sanity check" to backup your
>>>>>>>>>>>>>>>>>>>> DICOMS before/after running dcmodify, and use dcmdump on each version to
>>>>>>>>>>>>>>>>>>>> diff the outputs -- this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Re the protocol violation -- AcquisitionProtocol not
>>>>>>>>>>>>>>>>>>>> recognized or unknown : this means your scans did not match what is
>>>>>>>>>>>>>>>>>>>> stored in your mri_protocol table.
>>>>>>>>>>>>>>>>>>>> Check the MRI Violations front-end module -- can you
>>>>>>>>>>>>>>>>>>>> see why they didn't match?
>>>>>>>>>>>>>>>>>>>> Send us an example, in addition to the contents of the
>>>>>>>>>>>>>>>>>>>> mri_protocol table, if you can't find the source of the mismatch.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Here is the psc table
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I created 2 candidates profiles through the interface
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>> W: Found element (2005,1402) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>> W: Found element (2005,140f) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>>>>>>>> length, reading a sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> dcmodify at another Dicom didn't show warnings. Below
>>>>>>>>>>>>>>>>>>>> you can see the execution for the second dicom. Mnics could not be inserted
>>>>>>>>>>>>>>>>>>>> due to AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 12
>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name
>>>>>>>>>>>>>>>>>>>> '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>>>>>>>>>>>>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>> Database is available.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> You are creating a tar with the following command:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> tar -cf
>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> * Taken from dir :
>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>> * Archive target location :
>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1
>>>>>>>>>>>>>>>>>>>> * Name of host OS : Linux
>>>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin
>>>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-06
>>>>>>>>>>>>>>>>>>>> 18:36:50
>>>>>>>>>>>>>>>>>>>> * dicomSummary version : 1
>>>>>>>>>>>>>>>>>>>> * dicomTar version : 1
>>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball :
>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>> * md5sum for complete archive :
>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl
>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>> md5sum
>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> candidate id 602102
>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>>> inserting into the database: 2
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --> The minc file cannot be registered since the
>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol is unknown
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>>>>>>>>>>> *delete_imaging_upload* script --
>>>>>>>>>>>>>>>>>>>> details here:
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> What's in your *psc* table? (Is it properly
>>>>>>>>>>>>>>>>>>>> populated? This is a pre-requisite to loading imaging
>>>>>>>>>>>>>>>>>>>> data.
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>> The foreign key constraint error on the candidate
>>>>>>>>>>>>>>>>>>>> record is curious.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> There are also a few options for creating candidates
>>>>>>>>>>>>>>>>>>>> when inserting imaging data:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> -- Method 1 : in 2 steps with the API then DICOM
>>>>>>>>>>>>>>>>>>>> insertion pipeline
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> a. via the LORIS API -- Create the candidates (and
>>>>>>>>>>>>>>>>>>>> visits, optionally I think)
>>>>>>>>>>>>>>>>>>>> How to:
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Then as a second step:
>>>>>>>>>>>>>>>>>>>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets>
>>>>>>>>>>>>>>>>>>>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>> You will want to first ensure that the PatientName
>>>>>>>>>>>>>>>>>>>> header in the DICOMs as well as tar package are correctly labelled with
>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>> How to :
>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Be sure to use the *-c* and *-s* options when running
>>>>>>>>>>>>>>>>>>>> the bids_import script, to automatically create your
>>>>>>>>>>>>>>>>>>>> candidates and sessions.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> How do i delete a Study? And everytime do i have to
>>>>>>>>>>>>>>>>>>>> create a new candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> *First execution:*
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>> DBD::mysql::db do failed: Cannot add or update a child
>>>>>>>>>>>>>>>>>>>> row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>>>>>>>>>>>>>>>>>>> (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>> ERROR: Failed to insert record in table mri_scanner:
>>>>>>>>>>>>>>>>>>>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>> SET
>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>> Medical Systems';
>>>>>>>>>>>>>>>>>>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>> Error obtained:Cannot add or update a child row: a
>>>>>>>>>>>>>>>>>>>> foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>> `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> ERROR: The validation has failed. Either re-run the
>>>>>>>>>>>>>>>>>>>> validation again and fix the problem. Or re-run tarchiveLoader.pl using
>>>>>>>>>>>>>>>>>>>> -force to force the execution.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> PROBLEM:
>>>>>>>>>>>>>>>>>>>> The user 'lorisadmin' has already inserted this study.
>>>>>>>>>>>>>>>>>>>> The unique study ID is
>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>> This is the information retained from the first time
>>>>>>>>>>>>>>>>>>>> the study was inserted:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> * Taken from dir :
>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>> * Archive target location :
>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>> * Name of creating host : 127.0.1.1
>>>>>>>>>>>>>>>>>>>> * Name of host OS : Linux
>>>>>>>>>>>>>>>>>>>> * Created by user : lorisadmin
>>>>>>>>>>>>>>>>>>>> * Archived on : 2019-09-04
>>>>>>>>>>>>>>>>>>>> 18:33:05
>>>>>>>>>>>>>>>>>>>> * dicomSummary version : 1
>>>>>>>>>>>>>>>>>>>> * dicomTar version : 1
>>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball :
>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>> * md5sum for complete archive :
>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Last update of record:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Ok, this sounds like good progress. Let us know when
>>>>>>>>>>>>>>>>>>>> you next encounter issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>
>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>> I'll look into how we can better handle the incoming/
>>>>>>>>>>>>>>>>>>>> directory next time.
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>> is populated correctly except its port is 'port' : ''. Also i have
>>>>>>>>>>>>>>>>>>>> tested that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I executed the script again, because the only error i
>>>>>>>>>>>>>>>>>>>> had previously was that the /data/incoming folder didn't exist and there
>>>>>>>>>>>>>>>>>>>> are no errors reported back except of warnings <<mysql: [Warning] Using a
>>>>>>>>>>>>>>>>>>>> password on the command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> It's possible -- if the script was unable to connect to
>>>>>>>>>>>>>>>>>>>> the database during its execution (e.g. typo in the password), that would
>>>>>>>>>>>>>>>>>>>> explain the underpopulated Image path and Loris-MRI code path you saw in
>>>>>>>>>>>>>>>>>>>> the Config module.
>>>>>>>>>>>>>>>>>>>> It's hard to tell without seeing the output from your
>>>>>>>>>>>>>>>>>>>> script run -- Did you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting at line 222
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222>
>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> For example, check if the database connection
>>>>>>>>>>>>>>>>>>>> information was populated accurately in $mridir
>>>>>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is
>>>>>>>>>>>>>>>>>>>> an image with the configurations i typed. Maybe the problem is somewhere at
>>>>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working
>>>>>>>>>>>>>>>>>>>> and all the front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod
>>>>>>>>>>>>>>>>>>>> 775 project
>>>>>>>>>>>>>>>>>>>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Yes, it's important that project/ have 775 permissions
>>>>>>>>>>>>>>>>>>>> and that lorisadmin be part of the sudoers group, per step
>>>>>>>>>>>>>>>>>>>> 1 in the install Readme
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> > As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>>>>>>>> change LORIS to loris, right?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> These imaging paths will be updated during your
>>>>>>>>>>>>>>>>>>>> imaging installation
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Setup> by an
>>>>>>>>>>>>>>>>>>>> automated script -- you do not need to set them manually via the Config
>>>>>>>>>>>>>>>>>>>> module.
>>>>>>>>>>>>>>>>>>>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Setup> for
>>>>>>>>>>>>>>>>>>>> detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>>>>>>>> change LORIS to loris, right?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> i used
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>>>>>>>>>>>>>>>>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> you had suggested in the past, make worked and now i
>>>>>>>>>>>>>>>>>>>> can see all the contents in the web-interface, but i don't need make
>>>>>>>>>>>>>>>>>>>> install?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 14615 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0009.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 78106 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0010.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 51135 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0011.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 23443 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0012.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 10443 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0013.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 175139 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0014.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 42208 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0015.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 51987 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0016.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 42270 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191001/d4c0b4f3/attachment-0017.png>
More information about the Loris-dev
mailing list