[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Sun Sep 8 10:12:14 EDT 2019
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
>>
>
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