[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Sep 23 19:30:01 EDT 2019
Hi,
Here is our auto dicom uploading python script:
https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
To give you a brief idea:
Per folder it will:
1) Delete all the .bak files
2) Locate .dcm files and update the Patient header
3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, TE_max
parameters of T1 protocol and do an update at the mri_protocol table
https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
For some reason some files are missing SeriesDescription/ProtocolName
In total i have 7 folders
[image: image.png]
3/7 passed
[image: image.png]
Also about the first patient with DC0000 had a violation "T1 AXIAL SE
GADO", but my script didn't output a TE of 17 nowhere and i find that weird
since Loris detects the SeriesDescription.
[image: image.png]
Now about the 4/7 that didn't passed
102327840 and 102809579 outputs "The target directory does not contain a
single DICOM file.", therefore they are missing their StudyUID
102506134 has 2 studyuid "You can't use it with data from multiple studies."
and 102761034 "No data could be converted into valid MINC files. localizer,
scout will not be considered!" What is this?
If i wanted to force the insertion of 102327840, 102809579 and 102506134
can i just pass a flag parameter to batch_uploads_imageuploader.pl? or
modify imaging_upload_file.pl?
Thank you,
Sotirios
PS
To diagnose a folder search the name of the folder at dicom_output.txt.
Στις Παρ, 20 Σεπ 2019 στις 4:54 μ.μ., ο/η Christine Rogers, Ms. <
christine.rogers at mcgill.ca> έγραψε:
> Hi Sotirios,
> Glad to hear about your progress.
>
> Yes, the script you used to delete imaging data is fully documented here
> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md>
> -- let us know if you didn't find the answers you were looking for there.
> (Is it possible the null row in *mri_scanner* seen in your database
> management software is a visual placeholder for you as the user? I'm not
> sure why a scanner would ever be registered with ID='0' as your screenshot
> showed.)
>
> Best,
> Christine
>
> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> I fixed it with this
>>
>> [image: image.png]
>>
>> Στις Παρ, 20 Σεπ 2019 στις 4:37 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> έγραψε:
>>
>>> Hi,
>>>
>>> I tried to create a new candidate using the API, is there something
>>> wrong with the structure? why did i receive a 500 internal error? In the
>>> loris-error log it state that there is something wrong with token, but i
>>> verfied that the type of the token is a string.
>>>
>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client
>>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1
>>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string,
>>> null given, called in
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>> defined in
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>> SinglePointLogin->authenticate()\n#2
>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in
>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>
>>> [image: image.png]
>>>
>>> Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>>> 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
>>>>>
>>>> _______________________________________________
>> 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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(loris-mri-python) lorisadmin at loris-VirtualBox:~/DataQualityControlTool/mipqctool$ python dicom_uploader.py
./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000048_15169884000bff.dcm
102788419
Creating candidate
Update externalid
Create candidate
Candidate Info 868341 DCC0000
Next Visit Label 1
102788419
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 22 /data/incoming/DCC0000_868341_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-8\-pmFnoJ -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-8\-pmFnoJ \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-8-pmFnoJ
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-1-8-pmFnoJ
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-1-8-pmFnoJ.tar ImagingUpload-1-8-pmFnoJ
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-1-8-pmFnoJ
* Archive target location : /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-24 01:08:36
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 3a213c69e608266355f11494e8253c02 ImagingUpload-1-8-pmFnoJ.tar
* md5sum for DICOM tarball gzipped : 5740530dbe533d843884b1a4f86c7f83 ImagingUpload-1-8-pmFnoJ.tar.gz
* md5sum for complete archive : 946c5a419e46f49912cc586fc7522a9b DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.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_2015\-12\-22_ImagingUpload\-1\-8\-pmFnoJ\.tar -uploadID 22 -verbose
md5sum /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.tar
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
Set centerID = 1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
Number of MINC files that will be considered for inserting into the database: 5
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-8-pLTyn6.log
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_001.mnc
Creating NIfTI files
found zspace at 1 0
found yspace at 2 1
found xspace at 0 2
0 2 1 1 256 0.976562
1 1 2 1 256 0.976562
2 0 0 1 176 1.000000
Restructuring...
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-8-BlB4D6.log
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-aj183j.log
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_002.mnc
Creating NIfTI files
found zspace at 0 0
found yspace at 1 1
found xspace at 2 2
0 2 0 1 30 4.940154
1 1 1 1 256 0.976562
2 0 2 1 256 0.976562
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-pqkH2B.log
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_003.mnc
Creating NIfTI files
found zspace at 1 0
found yspace at 0 1
found xspace at 2 2
0 2 1 1 256 0.976562
1 1 0 1 30 5.233743
2 0 2 1 256 0.976562
Restructuring...
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-re4bXt.log
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
PSCID is: DCC0000
CandID id: 868341
visit_label is: V1
candidate id 868341
Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_004.mnc
Creating NIfTI files
found zspace at 1 0
found yspace at 2 1
found xspace at 0 2
0 2 1 1 256 0.976562
1 1 2 1 256 0.976562
2 0 0 1 30 4.465090
Restructuring...
noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_001.mnc
SNR is: 30.9451
noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_002.mnc
SNR is: 62.5745
noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_003.mnc
SNR is: 61.2643
noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_004.mnc
SNR is: 56.031
Creating Minc Pics
TarchiveSource is 11
Connecting to database.
FileID from mass_pic.pl is: 15
FileID from mass_pic.pl is: 16
FileID from mass_pic.pl is: 17
FileID from mass_pic.pl is: 18
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-1-8-Q5zNUp/ImagingUpload-1-8-pmFnoJ*
Can't exec "mail": No such file or directory at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 665.
print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 666.
print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 667.
print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 668.
print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 669.
find /data/loris/data/tarchive// -name *ImagingUpload-1-8-pmFnoJ*
rm /data/incoming/DCC0000_868341_V1.tar.gz
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
1940
./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000030_151783708598e6.dcm
102327840
Creating candidate
Update externalid
Create candidate
Candidate Info 627229 DCC0001
Next Visit Label 1
./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000088_1517837174996a.dcm does not have Protocolname
102327840
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 23 /data/incoming/DCC0001_627229_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-9\-gE48TD -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-gE48TD \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-9-gE48TD
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
The target directory does not contain a single DICOM file.
The dicomTar.pl execution has failed.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
600
./102809579/10/1.3.12.2.1107.5.2.30.27780.2017071115494453951663644.0.0.0_0010_000030_1518430122f026.dcm
102809579
Creating candidate
Update externalid
Create candidate
Candidate Info 167757 DCC0002
Next Visit Label 1
102809579
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 24 /data/incoming/DCC0002_167757_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-9\-71OIUb -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-71OIUb \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-9-71OIUb
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
The target directory does not contain a single DICOM file.
The dicomTar.pl execution has failed.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
1800
./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000009_15181073851a4d.dcm
000535670
Creating candidate
Update externalid
Create candidate
Candidate Info 210134 DCC0003
Next Visit Label 1
./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000111_151810731519ee.dcm does not have Protocolname
000535670
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 25 /data/incoming/DCC0003_210134_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-9\-XnnapL -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-XnnapL \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-9-XnnapL
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-1-9-XnnapL
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-1-9-XnnapL.tar ImagingUpload-1-9-XnnapL
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-1-9-XnnapL
* Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-1-9-XnnapL.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-24 01:09:33
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : af694b3303426fd5bc116be614ca4d68 ImagingUpload-1-9-XnnapL.tar
* md5sum for DICOM tarball gzipped : b0e25d740a22cf6b04548825f77577c7 ImagingUpload-1-9-XnnapL.tar.gz
* md5sum for complete archive : 54a456d222aa37b80bbedd3be843150e DCM_2012-12-05_ImagingUpload-1-9-XnnapL.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_2012\-12\-05_ImagingUpload\-1\-9\-XnnapL\.tar -uploadID 25 -verbose
md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-1-9-XnnapL.tar
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
candidate id 210134
Set centerID = 1
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
Number of MINC files that will be considered for inserting into the database: 1
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-mWwIoL.log
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
PSCID is: DCC0003
CandID id: 210134
visit_label is: V1
candidate id 210134
Finished file: assembly/210134/V1/mri/native/loris_210134_V1_t1_001.mnc
Creating NIfTI files
found zspace at 1 0
found yspace at 2 1
found xspace at 0 2
0 2 1 1 256 1.000000
1 1 2 1 256 1.000000
2 0 0 1 91 1.766667
Restructuring...
noise_estimate --snr /data/loris/data//assembly/210134/V1/mri/native/loris_210134_V1_t1_001.mnc
SNR is: 23.989
Creating Minc Pics
TarchiveSource is 12
Connecting to database.
FileID from mass_pic.pl is: 19
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-1-9-jRPp63/ImagingUpload-1-9-XnnapL*
find /data/loris/data/tarchive// -name *ImagingUpload-1-9-XnnapL*
rm /data/incoming/DCC0003_210134_V1.tar.gz
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
9.90050029754638
./000998448/205/1.3.46.670589.11.70598.5.0.7280.2016082207333647000_0205_000024_1518217540255b.dcm
000998448
Creating candidate
Update externalid
Create candidate
Candidate Info 183367 DCC0004
Next Visit Label 1
000998448
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 26 /data/incoming/DCC0004_183367_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-9\-aRk36X -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-aRk36X \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-9-aRk36X
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-1-9-aRk36X
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-1-9-aRk36X.tar ImagingUpload-1-9-aRk36X
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-1-9-aRk36X
* Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-24 01:10:01
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : ea44c342cc95679c8d1da95b0c2bb4d4 ImagingUpload-1-9-aRk36X.tar
* md5sum for DICOM tarball gzipped : 42971f1828c465ea9e4c87a4ccbcef14 ImagingUpload-1-9-aRk36X.tar.gz
* md5sum for complete archive : 9f7a31a61a15ee4b7f8cbadad7e94599 DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar
Adding archive info into database
DBD::mysql::st execute failed: Data truncated for column 'EchoTime' at row 1 at /data/loris/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 340.
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\-1\-9\-aRk36X\.tar -uploadID 26 -verbose
md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
candidate id 183367
Set centerID = 1
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
PSCID is: DCC0004
CandID id: 183367
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-1-10-RG9p3u.log
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
candidate id 183367
Finished file: assembly/183367/V1/mri/native/loris_183367_V1_t1_001.mnc
Creating NIfTI files
found zspace at 1 0
found yspace at 2 1
found xspace at 0 2
0 2 1 1 384 0.623811
1 1 2 1 384 0.623811
2 0 0 1 180 0.950000
Restructuring...
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-10-oy2BKe.log
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
PSCID is: DCC0004
CandID id: 183367
visit_label is: V1
candidate id 183367
Finished file: assembly/183367/V1/mri/native/loris_183367_V1_t1_002.mnc
Creating NIfTI files
found zspace at 0 0
found yspace at 1 1
found xspace at 2 2
0 2 0 1 29 4.660714
1 1 1 1 384 0.623811
2 0 2 1 384 0.623811
noise_estimate --snr /data/loris/data//assembly/183367/V1/mri/native/loris_183367_V1_t1_001.mnc
SNR is: 102.424
noise_estimate --snr /data/loris/data//assembly/183367/V1/mri/native/loris_183367_V1_t1_002.mnc
SNR is: 136.395
Creating Minc Pics
TarchiveSource is 13
Connecting to database.
FileID from mass_pic.pl is: 20
FileID from mass_pic.pl is: 21
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-1-10-_QDxoy/ImagingUpload-1-9-aRk36X*
find /data/loris/data/tarchive// -name *ImagingUpload-1-9-aRk36X*
rm /data/incoming/DCC0004_183367_V1.tar.gz
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
7.96409988403320
./102761034/301/1.3.46.670589.11.34037.5.0.4664.2016120612342878292_0301_000022_151699185019fa.dcm
102761034
Creating candidate
Update externalid
Create candidate
Candidate Info 651370 DCC0005
Next Visit Label 1
102761034
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 27 /data/incoming/DCC0005_651370_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-10\-oNM8vm -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-10\-oNM8vm \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-10-oNM8vm
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-1-10-oNM8vm
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-1-10-oNM8vm.tar ImagingUpload-1-10-oNM8vm
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-1-10-oNM8vm
* Archive target location : /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-24 01:10:57
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : b2932757fc7666efad789a82d43d706e ImagingUpload-1-10-oNM8vm.tar
* md5sum for DICOM tarball gzipped : a23f143d37f98f5126e9791919e08191 ImagingUpload-1-10-oNM8vm.tar.gz
* md5sum for complete archive : 8afe8a06f52d5ff956b4d97a7bd8ac8a DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.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\-12\-06_ImagingUpload\-1\-10\-oNM8vm\.tar -uploadID 27 -verbose
md5sum /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.tar
PSCID is: DCC0005
CandID id: 651370
visit_label is: V1
PSCID is: DCC0005
CandID id: 651370
visit_label is: V1
candidate id 651370
Set centerID = 1
PSCID is: DCC0005
CandID id: 651370
visit_label is: V1
PSCID is: DCC0005
CandID id: 651370
visit_label is: V1
Number of MINC files that will be considered for inserting into the database: 0
No data could be converted into valid MINC files.
localizer, scout will not be considered!
The tarchiveLoader.pl insertion script has failed.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
9.88119983673095
./102506134/401/1.3.46.670589.11.34037.5.0.4800.2015021615033196828_0401_000098_1517388840aea6.dcm
102506134
Creating candidate
Update externalid
Create candidate
Candidate Info 638739 DCC0006
Next Visit Label 1
102506134
Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
Running now the following command: /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 28 /data/incoming/DCC0006_638739_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-1\-11\-3ZZg0p -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-1\-11\-3ZZg0p \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-1-11-3ZZg0p
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
ERROR: This class is designed around the notion of a 'Study'.
You can't use it with data from multiple studies.
The following study UIDs were found:
'1.3.51.0.1.1.10.49.10.222.2753369.2752207'
'1.3.51.0.1.1.10.49.10.222.3332609.3331661'
The dicomTar.pl execution has failed.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250.
print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251.
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