[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Sep 27 06:17:36 EDT 2019
Hi,
the mri passed, for some reason it consumed 5.12GB of ram. Now about the
mri_violations, dicoms are triggered to be inserted there only if there is
a violation for Tr_min, Tr_max, in general for its header parameter?
Because i don't see the cases of 'No single dicom" or with the 2 studyiuid
to be there.
Thanks
Στις Πέμ, 26 Σεπ 2019 στις 5:07 μ.μ., ο/η Cecile Madjar <
cecile.madjar at mcin.ca> έγραψε:
> Hi Sotirios,
>
> Sorry to hear you are having issues with the memory. I think most of our
> VMs are set up with 4GB of RAM so with 4GB you should be fine.
>
> Hope this helps!
>
> Cécile
>
> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi,
>>
>> about that dicom that had that insertion error it's about 30mb and when
>> it is being processed the ram is being drastically increased from 2gb to
>> 3.28 and then the whole virtual machine is frozen. What is the recommended
>> size of ram for using Loris?
>>
>> Thanks
>>
>> [image: image.png]
>>
>>
>> Στις Τρί, 24 Σεπ 2019 στις 11:24 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> Hi Sotirios,
>>>
>>> Glad to see that the StudyUID problem was fixed!
>>>
>>> For the delete script issue, if you are absolutely certain that no
>>> processes are run for that uploadID, you can update the mri_upload table
>>> and set the column Inserting to 0 instead of 1 for that uploadID. It
>>> looks like for some reason the scripts did not update this field when it
>>> stopped the insertion. Not sure why that would be the case though.
>>> Note: only do that update if you are certain that there is no processing
>>> happening.
>>>
>>> Hope this helps!
>>>
>>>
>>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> about the Dicoms i reported that didn't have a StudyID they actually do
>>>>
>>>> [image: image.png]
>>>>
>>>>
>>>> [image: image.png]
>>>>
>>>> I thought that this might be a permission because "w" was missing at
>>>> the group. After using chmod -R 775 only 102809579 passed, but with no mnic
>>>> files. Also now i have this error
>>>>
>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$
>>>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>> Cannot delete upload 34: the MRI pipeline is currently processing it.
>>>>
>>>> How can solve this?
>>>>
>>>> Thanks
>>>>
>>>>
>>>> Στις Τρί, 24 Σεπ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> έγραψε:
>>>>
>>>>> 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
>>>>>>
>>>>> _______________________________________________
>>>> Loris-dev mailing list
>>>> Loris-dev at bic.mni.mcgill.ca
>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>
>>>
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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 282430 DCC0000
Next Visit Label 1
./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000158_15169884100c6f.dcm does not have Protocolname
./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000158_15169884100c6f.dcm does not have SeriesDescription
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 47 /data/incoming/DCC0000_282430_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-55\-UvVoD1 -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-55\-UvVoD1 \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-55-UvVoD1
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-4-55-UvVoD1
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-4-55-UvVoD1.tar ImagingUpload-4-55-UvVoD1
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-4-55-UvVoD1
* Archive target location : /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-27 04:55:32
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 14adb7eef8c44ba8155bd21ba53c7ccc ImagingUpload-4-55-UvVoD1.tar
* md5sum for DICOM tarball gzipped : 0761dd6b8cd49b6f47041c3fdb91c36f ImagingUpload-4-55-UvVoD1.tar.gz
* md5sum for complete archive : 780bc49bbbb615f17f338fb34afcb40f DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.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\-4\-55\-UvVoD1\.tar -uploadID 47 -verbose
md5sum /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.tar
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
Set centerID = 1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
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-4-55-NF3beZ.log
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
Finished file: assembly/282430/V1/mri/native/loris_282430_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 1 175 1.005747
Restructuring...
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-3SdUJ3.log
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-ascm1w.log
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
Finished file: assembly/282430/V1/mri/native/loris_282430_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-4-55-PIcp0N.log
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
Finished file: assembly/282430/V1/mri/native/loris_282430_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-4-55-cY5KRd.log
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
PSCID is: DCC0000
CandID id: 282430
visit_label is: V1
candidate id 282430
Finished file: assembly/282430/V1/mri/native/loris_282430_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/282430/V1/mri/native/loris_282430_V1_t1_001.mnc
SNR is: 30.8967
noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_002.mnc
SNR is: 62.5745
noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_003.mnc
SNR is: 61.2643
noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_004.mnc
SNR is: 56.031
Creating Minc Pics
TarchiveSource is 25
Connecting to database.
FileID from mass_pic.pl is: 44
FileID from mass_pic.pl is: 45
FileID from mass_pic.pl is: 46
FileID from mass_pic.pl is: 47
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-4-55-BWCHDs/ImagingUpload-4-55-UvVoD1*
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-4-55-UvVoD1*
rm /data/incoming/DCC0000_282430_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 122941 DCC0001
Next Visit Label 1
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 48 /data/incoming/DCC0001_122941_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-56\-JBLS6f -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-56\-JBLS6f \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-56-JBLS6f
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 153533 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 49 /data/incoming/DCC0002_153533_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-56\-djVIXf -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-56\-djVIXf \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-56-djVIXf
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-4-56-djVIXf
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-4-56-djVIXf.tar ImagingUpload-4-56-djVIXf
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-4-56-djVIXf
* Archive target location : /data/loris/data/tarchive/DCM_2017-07-11_ImagingUpload-4-56-djVIXf.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-27 04:56:16
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 5f55a5556596ed5f44b0f908711a7114 ImagingUpload-4-56-djVIXf.tar
* md5sum for DICOM tarball gzipped : 2bf98abfdaf85756cc5f2ccca7eca152 ImagingUpload-4-56-djVIXf.tar.gz
* md5sum for complete archive : 5eadd7a9f46d7574f1cdf15b2509fef8 DCM_2017-07-11_ImagingUpload-4-56-djVIXf.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_2017\-07\-11_ImagingUpload\-4\-56\-djVIXf\.tar -uploadID 49 -verbose
md5sum /data/loris/data/tarchive/DCM_2017-07-11_ImagingUpload-4-56-djVIXf.tar
PSCID is: DCC0002
CandID id: 153533
visit_label is: V1
PSCID is: DCC0002
CandID id: 153533
visit_label is: V1
candidate id 153533
Set centerID = 1
PSCID is: DCC0002
CandID id: 153533
visit_label is: V1
PSCID is: DCC0002
CandID id: 153533
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-4-56-Jwsdtf.log
PSCID is: DCC0002
CandID id: 153533
visit_label is: V1
PSCID is: DCC0002
CandID id: 153533
visit_label is: V1
candidate id 153533
Finished file: assembly/153533/V1/mri/native/loris_153533_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 1 640 0.437500
1 1 2 1 540 0.437500
2 0 0 1 43 1.000000
Restructuring...
noise_estimate --snr /data/loris/data//assembly/153533/V1/mri/native/loris_153533_V1_t1_001.mnc
SNR is: 206.057
Creating Minc Pics
TarchiveSource is 26
Connecting to database.
FileID from mass_pic.pl is: 48
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-4-56-adLn78/ImagingUpload-4-56-djVIXf*
find /data/loris/data/tarchive// -name *ImagingUpload-4-56-djVIXf*
rm /data/incoming/DCC0002_153533_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.
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 756939 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
./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000111_151810731519ee.dcm does not have SeriesDescription
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 50 /data/incoming/DCC0003_756939_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-58\-yNHgRZ -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-58\-yNHgRZ \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-58-yNHgRZ
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-4-58-yNHgRZ
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-4-58-yNHgRZ.tar ImagingUpload-4-58-yNHgRZ
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-4-58-yNHgRZ
* Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-27 04:58:35
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : c7b421c10fa2c6b4db057d2c942da9d4 ImagingUpload-4-58-yNHgRZ.tar
* md5sum for DICOM tarball gzipped : c14ee5bab7cc0e91884911fc50a72e6f ImagingUpload-4-58-yNHgRZ.tar.gz
* md5sum for complete archive : ff1de3b94301c8b0ace9d13d057c0ccc DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.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\-4\-58\-yNHgRZ\.tar -uploadID 50 -verbose
md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.tar
PSCID is: DCC0003
CandID id: 756939
visit_label is: V1
PSCID is: DCC0003
CandID id: 756939
visit_label is: V1
candidate id 756939
Set centerID = 1
PSCID is: DCC0003
CandID id: 756939
visit_label is: V1
PSCID is: DCC0003
CandID id: 756939
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-4-58-clwvUZ.log
PSCID is: DCC0003
CandID id: 756939
visit_label is: V1
PSCID is: DCC0003
CandID id: 756939
visit_label is: V1
candidate id 756939
Finished file: assembly/756939/V1/mri/native/loris_756939_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/756939/V1/mri/native/loris_756939_V1_t1_001.mnc
SNR is: 23.989
Creating Minc Pics
TarchiveSource is 27
Connecting to database.
FileID from mass_pic.pl is: 49
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-4-58-buXWmO/ImagingUpload-4-58-yNHgRZ*
find /data/loris/data/tarchive// -name *ImagingUpload-4-58-yNHgRZ*
rm /data/incoming/DCC0003_756939_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 280768 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 51 /data/incoming/DCC0004_280768_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-58\-JfECYF -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-58\-JfECYF \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-58-JfECYF
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-4-58-JfECYF
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-4-58-JfECYF.tar ImagingUpload-4-58-JfECYF
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-4-58-JfECYF
* Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-4-58-JfECYF.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-27 04:59:01
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 6d21df8cc0996eafa317f6ac9cc64123 ImagingUpload-4-58-JfECYF.tar
* md5sum for DICOM tarball gzipped : a198063eb18cfa4dc0591357c20dd1c2 ImagingUpload-4-58-JfECYF.tar.gz
* md5sum for complete archive : 3aad64442f6f8233690e645c4fd05fc5 DCM_2016-08-22_ImagingUpload-4-58-JfECYF.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\-4\-58\-JfECYF\.tar -uploadID 51 -verbose
md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-4-58-JfECYF.tar
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
candidate id 280768
Set centerID = 1
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
PSCID is: DCC0004
CandID id: 280768
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-4-59-NFKgPt.log
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
candidate id 280768
Finished file: assembly/280768/V1/mri/native/loris_280768_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-4-59-EbeiH8.log
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
PSCID is: DCC0004
CandID id: 280768
visit_label is: V1
candidate id 280768
Finished file: assembly/280768/V1/mri/native/loris_280768_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/280768/V1/mri/native/loris_280768_V1_t1_001.mnc
SNR is: 102.424
noise_estimate --snr /data/loris/data//assembly/280768/V1/mri/native/loris_280768_V1_t1_002.mnc
SNR is: 136.395
Creating Minc Pics
TarchiveSource is 28
Connecting to database.
FileID from mass_pic.pl is: 50
FileID from mass_pic.pl is: 51
Finished mass_pic.pl execution
Cleaning up temp files: rm -rf /tmp/TarLoad-4-59-P26NrA/ImagingUpload-4-58-JfECYF*
find /data/loris/data/tarchive// -name *ImagingUpload-4-58-JfECYF*
rm /data/incoming/DCC0004_280768_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 592193 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 52 /data/incoming/DCC0005_592193_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-4\-59\-udVPCy -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-4\-59\-udVPCy \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-4-59-udVPCy
Target: /data/loris/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-4-59-udVPCy
You are creating a tar with the following command:
tar -cf /data/loris/data/tarchive/ImagingUpload-4-59-udVPCy.tar ImagingUpload-4-59-udVPCy
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-4-59-udVPCy
* Archive target location : /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-4-59-udVPCy.tar
* Name of creating host : 127.0.1.1
* Name of host OS : Linux
* Created by user : lorisadmin
* Archived on : 2019-09-27 04:59:51
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : f56ffbbc4a49d937d401291b5dfdcc5d ImagingUpload-4-59-udVPCy.tar
* md5sum for DICOM tarball gzipped : 6b5ded248549f251c3c874a285bc7691 ImagingUpload-4-59-udVPCy.tar.gz
* md5sum for complete archive : a1fa979684d637c23d6a6fc7d4266bd3 DCM_2016-12-06_ImagingUpload-4-59-udVPCy.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\-4\-59\-udVPCy\.tar -uploadID 52 -verbose
md5sum /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-4-59-udVPCy.tar
PSCID is: DCC0005
CandID id: 592193
visit_label is: V1
PSCID is: DCC0005
CandID id: 592193
visit_label is: V1
candidate id 592193
Set centerID = 1
PSCID is: DCC0005
CandID id: 592193
visit_label is: V1
PSCID is: DCC0005
CandID id: 592193
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 976678 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 53 /data/incoming/DCC0006_976678_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-5\-0\-nJMgpV -name '__MACOSX' -delete
dicomTar.pl \/tmp\/ImagingUpload\-5\-0\-nJMgpV \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
Source: /tmp/ImagingUpload-5-0-nJMgpV
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:
'1.3.51.0.1.1.10.49.10.222.3332609.3331661'
'1.3.51.0.1.1.10.49.10.222.2753369.2752207'
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.
9.87489986419677
2500.1000
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