[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Sun Sep 8 10:12:52 EDT 2019
*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
>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 61107 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0010.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 42220 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0011.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 29279 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0012.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 78077 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0013.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 5647 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0014.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 5819 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0015.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 135445 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0016.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 16405 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0017.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 44301 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0018.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 84052 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20190908/5ae1d93e/attachment-0019.png>
More information about the Loris-dev
mailing list