[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Sep 30 06:00:01 EDT 2019
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
>>>>>>
>>>>>
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