[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Sep 13 09:43:21 EDT 2019
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
>>
>
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