[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Sep 20 09:44:37 EDT 2019
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
>>>
>>
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