[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Sun Sep 8 09:17:08 EDT 2019
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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