[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Sep 9 21:00:42 EDT 2019
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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