[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Sep 20 07:39:36 EDT 2019
Hi,
Is there a way also to delete candidates? Just to let you know what i did
to clear candidates, because maybe i may have missed dependencies.
First i deleted all their uploads
./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit the
backup file ? )
Afterwards i had some scanner candidates, so i deleted all the entries from
mri_scanner except that i couldn't delete this entry with the 0 ID.
[image: image.png]
Lastly i deleted the session and then the candidate table.
Thanks
Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine Rogers, Ms. <
christine.rogers at mcgill.ca> έγραψε:
> Hi Sotirios,
>
> We recommend that you use our existing tools for creating new candidates -
> either the LORIS API or if you are using a PHP script, by calling the Candidate
> class's createNew()
> <https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200>function.
> These will create the necessary records for you. (It's not recommended to
> make direct modifications to mysql database tables in your script, if I
> understand you.)
>
> The CandID should be a randomized 6 digit randomized ID, and there are
> multiple reasons for this.
> You can use the PSCID for project-specific IDs and the External ID field
> in the candidate table can also be used for any values you like.
> Additionally, any number of custom IDs can be added in parallel - these
> are entered/visible in the Candidate Information module and added in the
> back-end as candidate parameters.
>
> Best,
> Christine
>
>
>
> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi,
>>
>> We are building a script that will auto insert the candidates based on
>> their ExternalID. We would like to know whethere when we are creating a new
>> profile in the candidate table, if we also have to insert a new record at
>> another table? Furthermore is there a problem that in our case CandID won't
>> be a 6digit? ( should we start it from 100000?)
>>
>> Thanks
>>
>> [image: image.png]
>>
>>
>> Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault, Mrs <
>> melanie.legault2 at mcgill.ca> έγραψε:
>>
>>> That would normally be the case but the numeric part of the PSCID get
>>> paded with 0 on the left.
>>>
>>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char
>>> with a min value of 1, the sequence would be:
>>>
>>> ABC0001
>>> ABC0002
>>> ...
>>> ABC0010
>>> ...
>>>
>>> thus sorting them ascending will always get the latest value generated
>>> as the max value.
>>>
>>> Mélanie
>>>
>>> ------------------------------
>>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>> *Sent:* September 13, 2019 10:15
>>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>> loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>
>>> I see, although the PSCID value is varchar(255), it must be stored
>>> within a specific length of characters. Otherwise if we were to sort
>>> strings with different lengths the result would not be sorted correctly (
>>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>
>>> Thanks
>>>
>>> Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie Legault, Mrs <
>>> melanie.legault2 at mcgill.ca> έγραψε:
>>>
>>> Hello Sotirios,
>>>
>>> There is no `last value` stored anywhere.
>>> The code simply look for the PSCID with the max value and increase that
>>> value by 1 in order to generate the next PSCID.
>>>
>>> Hope this info help.
>>>
>>> Mélanie Legault | Software developer | Faculty of Medicine | McGill
>>> University
>>> 3801 University, Montréal, QC H3A 2B4
>>>
>>> ------------------------------
>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios
>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>> *Sent:* September 13, 2019 9:43
>>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>
>>> Hi,
>>>
>>> how does Loris determine the next available PSCID value for a new
>>> candidate? https://github.com/aces/Loris/wiki/Project-Customization
>>> e.x in the default case the PSCID is sequential, but where do we store the
>>> last value for the sequential sequence?
>>>
>>> Thanks
>>>
>>> Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>> Hi,
>>>
>>> the parameters in the mri_protocol you have assigned are global
>>> standard? or were assigned after trial and error?
>>>
>>> Thanks
>>>
>>> Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> Given you have done the initial setup of your tables to match your
>>> intended protocol/parameters according to instructions --
>>> the Troubleshooting guide documentation recommends
>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes>
>>> re-running the pipeline (and first deleting prior uploads).
>>>
>>> Best,
>>> Christine
>>>
>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> *if i were to change their status to resolve what would happen?
>>>
>>> Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>> I noticed that i can view the mnics at the brainbrowser from the
>>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/
>>> if i were to click their issue to resolve what would happend? would they
>>> appear in the dicom_archive view too? ).
>>>
>>>
>>>
>>> Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>> Hi,
>>>
>>> The defaut values of the schema exists in my local database. If i adjust
>>> the default values of TR_min and TE_min the mincs will be uploaded?
>>>
>>> [image: image.png]
>>>
>>>
>>> [image: image.png]
>>>
>>> Thanks
>>>
>>> Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> Is it possible that you haven't set up your mri_protocol table ? (and
>>> mri_scan_type table too, for additional types of scans)
>>>
>>> Like the psc table, this is a pre-requisite for the Imaging insertion
>>> setup : See the install/setup documentation :
>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>
>>> To add new rows, just use MySQL insert statements. You can adapt the
>>> insert statements which load the default table values --> e.g. Here on
>>> GitHub :
>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>> (see also the mri_scan_type table)
>>>
>>> Best,
>>> Christine
>>>
>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> I see that i can edit the values but not how to insert new rows.
>>>
>>> [image: image.png]
>>>
>>> If i choose Inserted with flag then will the minc be inserted?
>>>
>>> [image: image.png]
>>>
>>> Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> Glad to hear that *dcmodify* worked correctly.
>>>
>>> For the MRI Violations module, the screenshot is enough.
>>>
>>> It says "could not identify scan type", which we knew already. Did you
>>> click on the link on those words?
>>>
>>> It will take you to the next page of the module, showing for each scan
>>> what the scan parameters were, and will also show for comparison what's
>>> stored in your *mri_protocol* table.
>>> Compare these values to find which parameter was not correct according
>>> to your *mri_protocol* table scan type definitions.
>>>
>>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE)
>>> for scans.
>>> This can be done in the front-end, by editing the database table
>>> directly in the same subpage of the MRI Violations module.
>>>
>>> The MRI Violations module features are explained in more detail in the
>>> Help text for this module inside LORIS (click the ["?"] icon in the menu
>>> bar.)
>>>
>>> See also: Loris-MRI troubleshooting guide
>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md>
>>> : no MINCs inserted- violated scans
>>>
>>> Best,
>>> Christine
>>>
>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> looks like my previous email's attachment wasn't delivered due to
>>> security reasons, i uploaded my file at google drive
>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>
>>> Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>> Hi,
>>>
>>> From Dicat's view seems that dcmodify worked in both cases
>>>
>>> [image: image.png]
>>>
>>> [image: image.png]
>>>
>>> For the mri_violations i attached the .html output from webbrowser, so
>>> that you can check the filelds easier.
>>>
>>> [image: image.png]
>>>
>>> Thanks
>>>
>>>
>>>
>>> Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios --
>>> Great, sounds like more progress.
>>>
>>> About the dcmodify command -- I'm not sure why you're getting an Endian
>>> warning. (it's a warning not an error, correct?)
>>> To clarify -- Were the DICOM headers (PatientName) all successfully
>>> relabelled, after the command ran?
>>>
>>> You can use also our DICAT tool (https://github.com/aces/DICAT) to
>>> verify and/or update local DICOM headers -- though your dcmodify command is
>>> a great and fast solution for bulk header updates.
>>>
>>> If you're concerned about fields being changed (e.g. "(2001,105f)" from
>>> the warning message) - you can also dcmdump a DICOM slice before and look
>>> at these fields specifically.
>>> It's also not a bad "sanity check" to backup your DICOMS before/after
>>> running dcmodify, and use dcmdump on each version to diff the outputs --
>>> this will pinpoint what changed.
>>>
>>> Re the protocol violation -- AcquisitionProtocol not recognized or
>>> unknown : this means your scans did not match what is stored in your
>>> mri_protocol table.
>>> Check the MRI Violations front-end module -- can you see why they didn't
>>> match?
>>> Send us an example, in addition to the contents of the mri_protocol
>>> table, if you can't find the source of the mismatch.
>>>
>>> Best,
>>> Christine
>>>
>>>
>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> Here is the psc table
>>> [image: image.png]
>>>
>>> I created 2 candidates profiles through the interface
>>>
>>> [image: image.png]
>>>
>>> then runned dcmodify command to a dicom file
>>>
>>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>
>>> and got those warning: is this okay?
>>> W: Found element (2001,105f) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>> W: Found element (2005,1083) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>> W: Found element (2005,1402) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>> W: Found element (2005,140f) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>> W: Found element (2001,105f) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>> W: Found element (2005,1083) with VR UN and undefined length, reading a
>>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>
>>> dcmodify at another Dicom didn't show warnings. Below you can see the
>>> execution for the second dicom. Mnics could not be inserted due to
>>> AcquisitionProtocol being unknown.
>>>
>>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/
>>> imaging_upload_file.pl -profile prod -upload_id 12
>>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>
>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>> -delete
>>>
>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>> Target: /data/loris/data/tarchive
>>>
>>> Testing for database connectivity.
>>> Database is available.
>>>
>>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>
>>> You are creating a tar with the following command:
>>>
>>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>> ImagingUpload-18-36-mTrxXs
>>>
>>>
>>> getting md5sums and gzipping!!
>>>
>>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs
>>> * Archive target location :
>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>> * Name of creating host : 127.0.1.1
>>> * Name of host OS : Linux
>>> * Created by user : lorisadmin
>>> * Archived on : 2019-09-06 18:36:50
>>> * dicomSummary version : 1
>>> * dicomTar version : 1
>>> * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814
>>> ImagingUpload-18-36-mTrxXs.tar
>>> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f
>>> ImagingUpload-18-36-mTrxXs.tar.gz
>>> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e
>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>
>>> Adding archive info into database
>>>
>>> Removing temporary files from target location
>>>
>>>
>>> Done adding archive info into database
>>>
>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>> -profile prod
>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>> -uploadID 12 -verbose
>>> md5sum
>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> candidate id 602102
>>> Set centerID = 1
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>>
>>> Number of MINC files that will be considered for inserting into the
>>> database: 2
>>>
>>> log dir is /data/loris/data//logs and log file is
>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> candidate id 602102
>>>
>>> log dir is /data/loris/data//logs and log file is
>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> PSCID is: DCC0001
>>> CandID id: 602102
>>> visit_label is: V1
>>> candidate id 602102
>>>
>>> Cleaning up temp files: rm -rf
>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>
>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat
>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>
>>> ==> Loading file from disk
>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>
>>> --> mapping DICOM parameter for
>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>
>>> ==> computing md5 hash for MINC body.
>>>
>>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>
>>> ==> verifying acquisition protocol
>>>
>>> Acquisition protocol is unknown
>>>
>>> --> The minc file cannot be registered since the AcquisitionProtocol
>>> is unknown
>>>
>>> Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios:
>>>
>>> Sure -- you can delete imaging datasets with the *delete_imaging_upload*
>>> script --
>>> details here:
>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>
>>> What's in your *psc* table? (Is it properly populated? This is a
>>> pre-requisite to loading imaging data.
>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>> )
>>> The foreign key constraint error on the candidate record is curious.
>>>
>>> There are also a few options for creating candidates when inserting
>>> imaging data:
>>>
>>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline
>>>
>>> a. via the LORIS API -- Create the candidates (and visits, optionally I
>>> think)
>>> How to:
>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>
>>> Then as a second step:
>>> b. Use the imaging insertion pipeline
>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets>
>>> to load your DICOMs.
>>> You will want to first ensure that the PatientName header in the DICOMs
>>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel
>>>
>>> -- Method 2: for BIDS-format datasets:
>>> How to :
>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>
>>> Be sure to use the *-c* and *-s* options when running the bids_import script,
>>> to automatically create your candidates and sessions.
>>>
>>> Best,
>>> Christine
>>>
>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> How do i delete a Study? And everytime do i have to create a new
>>> candidate to get DCCID and a PSCID?
>>>
>>> *First execution:*
>>>
>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./
>>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt >
>>> log.txt
>>> Use of uninitialized value $_ in pattern match (m//) at ./
>>> batch_uploads_imageuploader.pl line 144.
>>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign
>>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at
>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>> ERROR: Failed to insert record in table mri_scanner:
>>> The following database commands failed:
>>> PREPARE s FROM 'INSERT INTO mri_scanner
>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>> SET
>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>> Medical Systems';
>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>> Error obtained:Cannot add or update a child row: a foreign key
>>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1`
>>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>>>
>>> ERROR: The validation has failed. Either re-run the validation again
>>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force the
>>> execution.
>>>
>>>
>>> The tarchiveLoader.pl insertion script has failed.
>>> Can't exec "mail": No such file or directory at ./
>>> batch_uploads_imageuploader.pl line 249.
>>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl
>>> line 250.
>>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl
>>> line 251.
>>>
>>>
>>> *And second execution: *
>>>
>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./
>>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt >
>>> log.txt
>>> Use of uninitialized value $_ in pattern match (m//) at ./
>>> batch_uploads_imageuploader.pl line 144.
>>>
>>> PROBLEM:
>>> The user 'lorisadmin' has already inserted this study.
>>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>> This is the information retained from the first time the study was
>>> inserted:
>>>
>>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy
>>> * Archive target location :
>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>> * Name of creating host : 127.0.1.1
>>> * Name of host OS : Linux
>>> * Created by user : lorisadmin
>>> * Archived on : 2019-09-04 18:33:05
>>> * dicomSummary version : 1
>>> * dicomTar version : 1
>>> * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d
>>> ImagingUpload-18-33-Qq7HGy.tar
>>> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec
>>> ImagingUpload-18-33-Qq7HGy.tar.gz
>>> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053
>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>
>>>
>>> Last update of record:
>>>
>>>
>>>
>>> The dicomTar.pl execution has failed.
>>> Can't exec "mail": No such file or directory at ./
>>> batch_uploads_imageuploader.pl line 249.
>>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl
>>> line 250.
>>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl
>>> line 251.
>>>
>>> Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> Ok, this sounds like good progress. Let us know when you next encounter
>>> issues as you progress through the Imaging Install/Setup docs
>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>.
>>> I'll look into how we can better handle the incoming/ directory next
>>> time.
>>> Best,
>>> Christine
>>>
>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>> populated correctly except its port is 'port' : ''. Also i have tested
>>> that i can connect to MySQL with lorisuser.
>>>
>>> I executed the script again, because the only error i had previously was
>>> that the /data/incoming folder didn't exist and there are no errors
>>> reported back except of warnings <<mysql: [Warning] Using a password on the
>>> command line interface can be insecure>>.
>>>
>>>
>>> Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> It's possible -- if the script was unable to connect to the database
>>> during its execution (e.g. typo in the password), that would explain the
>>> underpopulated Image path and Loris-MRI code path you saw in the Config
>>> module.
>>> It's hard to tell without seeing the output from your script run -- Did
>>> you see a sign of any such error?
>>> The Config fields are populated by the imaging_install.sh script (starting
>>> at line 222
>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222>
>>> )
>>>
>>> For example, check if the database connection information was populated
>>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py
>>>
>>> Best,
>>> Christine
>>>
>>>
>>>
>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> Hi Christine,
>>>
>>> If you are referring to the imaging_install.sh here is an image with the
>>> configurations i typed. Maybe the problem is somewhere at the last part
>>> which asks to configure as much as possible automatically?
>>>
>>> Thanks
>>>
>>>
>>> Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>> Hi Sotirios,
>>>
>>> Glad to hear your LORIS core install is up and working and all the
>>> front-end pages are loading.
>>>
>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project
>>> > and the web interface worked.
>>>
>>> Yes, it's important that project/ have 775 permissions and that
>>> lorisadmin be part of the sudoers group, per step 1 in the install
>>> Readme <https://github.com/aces/Loris#install-steps>.
>>>
>>> > As for the Paths, LORIS-MRI code and Image should change LORIS to
>>> loris, right?
>>>
>>> These imaging paths will be updated during your imaging installation
>>> <https://github.com/aces/Loris/wiki/Setup> by an automated script --
>>> you do not need to set them manually via the Config module.
>>> Please continue to follow the Setup Guide
>>> <https://github.com/aces/Loris/wiki/Setup> for detailed steps to follow.
>>>
>>> Best,
>>> Christine
>>>
>>>
>>>
>>>
>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris,
>>> right?
>>>
>>> [image: image.png]
>>>
>>>
>>> Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>> Hi,
>>>
>>> i used
>>>
>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>> sudo apt-get install -y nodejs
>>>
>>>
>>> you had suggested in the past, make worked and now i can see all the
>>> contents in the web-interface, but i don't need make install?
>>>
>>> Thanks
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>>
>>> --
>>>
>>> christine.rogers at mcgill.ca
>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>> Montreal Neurological Institute
>>> McGill University | Montreal | Canada
>>>
>>> _______________________________________________
>> 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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