[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Wed Nov 13 16:22:23 EST 2019
HI Yang,
We make use of pydicom library too. Now about the validate.py i see that
you check if some attributes are missing such as PatientID, PatientName
which all of our files contains that info. Maybe i have missed something on
the setup of my other virtual machine ( although one dicom passed on the
new vm successfully, the others that were inserted correctly on my old vm
fails on the new one ), i think that i had asked about this error "Use of
uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
batch_uploads_imageuploader.pl line 144." but i don't remember the solution.
Thanks
Στις Τετ, 13 Νοε 2019 στις 5:45 π.μ., ο/η Yang Ding <it at cnbp.ca> έγραψε:
> Hey, Sotirios,
>
> Christine from the LORIS team mentioned you had some issue with DICOM. I
> am a fellow developer for an external project using LORIS, kind of just
> like you. We had to implement DICOM upload as well but more as a fully
> automated pipeline actually.
>
> While we were building CNBP, we had coded up some minor Python functions
> to check DICOM integrity (and simple validations) and you might be able to
> gain some inspiration from it and help you with your cause. For more
> comprehensive solution, PyDICOM (
> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems
> like a descent python package to help out with a lot of DICOM data checks
> (I was essentially just building customized wrapper calls to them). You can
> see some example scripts here as part of our DICOM submodule. It is pretty
> rough around the edges but hopefully point you in the right direcitons
> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>
> Cheers,
>
> Yang Ding, PhD.
> Canadian Neonatal Brain Platform Architect
>
> On Tue, Nov 12, 2019 at 8:29 AM <loris-dev-request at bic.mni.mcgill.ca>
> wrote:
>
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>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>> From: Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>> Cc: loris-dev at bic.mni.mcgill.ca
>> Subject: Re: [Loris-dev] Import mri - scripts
>> Message-ID:
>> <CAKHj7uST=
>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi,
>>
>> Could we send you a link with 10 anonymized dicom files to diagnose the
>> warnings we get?
>>
>> Thanks
>>
>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> ??????:
>>
>> > Hi Cecile,
>> >
>> > We were wondering whether Loris has a tool to check if there are
>> problems
>> > with the dcm files, before trying to upload them. Something that could
>> > provide the same results provided in the warning_output, this is the
>> > summary from the mri_upload at the front-page. Also which attributes of
>> the
>> > dcm header would trigger a warning? is there a dcm file header
>> > specification for Loris?
>> >
>> > Thanks
>> >
>> > Sotirios
>> >
>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> > sotirisnik at gmail.com> ??????:
>> >
>> >> Hi,
>> >>
>> >> Yes, by parsing now() into unix_timestamp function it worked,but i
>> >> thought that something else was causing the 2nd issue.
>> >> Thanks
>> >>
>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, <
>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>> >>
>> >>> Hi Sotirios,
>> >>>
>> >>> The first error occurs because the QCFirstChangeTime and columns are
>> of
>> >>> type `unsigned integer` and not `datatime`. You should be using
>> >>> UNIX_TIMESTAMP() instead of NOW().
>> >>>
>> >>> The second error occurs because the trigger triggers a rollback of the
>> >>> insert statement in the files table.
>> >>> See mysql documentation for trigger error handling.
>> >>>
>> >>> An error during either a BEFORE or AFTER trigger results in failure of
>> >>> the entire statement that caused trigger invocation.
>> >>>
>> >>>
>> >>> Thank you for sharing that. I hope it helps.
>> >>> -- Xavier
>> >>>
>> >>> ------------------------------
>> >>> *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:* October 1, 2019 8:33 AM
>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>;
>> >>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>> >>>
>> >>> When mincs are inserted their corresponding rows at the file table are
>> >>> inserted too
>> >>> [image: image.png]
>> >>>
>> >>> i would like to insert their rows at file_qcstatus as well, because i
>> >>> don't want manually to label them as passed throught the interface
>> >>>
>> >>> [image: image.png]
>> >>>
>> >>>
>> >>> That is the trigger i wrote
>> >>>
>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT`
>> AFTER
>> >>> INSERT ON `files` FOR EACH ROW
>> >>> BEGIN
>> >>> INSERT INTO files_qcstatus
>> >>> SET FileID = NEW.FileID,
>> >>> SeriesUID = NEW.SeriesUID,
>> >>> EchoTime = NEW.EchoTime,
>> >>> QCStatus = "Pass",
>> >>> QCFirstChangeTime = NOW(),
>> >>> QCLastChangeTime = NOW();
>> >>> END
>> >>>
>> >>> although it contains some errors
>> >>>
>> >>> DBD::mysql::db do failed: Out of range value for column
>> >>> 'QCFirstChangeTime' at row 1 at
>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign
>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files`
>> (`FileID`))
>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar <
>> >>> cecile.madjar at mcin.ca> ??????:
>> >>>
>> >>> Hi Sotirios,
>> >>>
>> >>> In the mri_upload table, there is a TarchiveID column associated with
>> >>> the MRI upload you inserted. When this value is NULL, it means no
>> DICOMs
>> >>> were inserted into the tarchive tables. At the end of the insertion
>> of the
>> >>> DICOMs in the tarchive tables, this value is updated with the correct
>> >>> TarchiveID associated with the upload.
>> >>>
>> >>> Could this correspond to what you want to do?
>> >>>
>> >>> Regarding the files_qcstatus, this table is only linked to the files
>> >>> table (hence, the MINC files). You could always create a new table for
>> >>> dicom_qcstatus and link it to the tarchive table?
>> >>>
>> >>> C?cile
>> >>>
>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> wrote:
>> >>>
>> >>> Hi,
>> >>>
>> >>> i would like whenever a dicom is imported to mark all their
>> >>> coressponding qc_status to "pass". I was thinking of creating a
>> trigger for
>> >>> that, but which tables do i need to add entries to? So far from what
>> i see
>> >>> i need to add entres at the table "files" whenever an insertion
>> happens to
>> >>> files_qcstatus.
>> >>>
>> >>> Thanks
>> >>>
>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my
>> email
>> >>> i sent 3 hours ago (not StudyUID).
>> >>>
>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> Hi,
>> >>>
>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am
>> >>> looking for is not stored in the database?
>> >>>
>> >>> [image: image.png]
>> >>>
>> >>> Thanks.
>> >>>
>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar <
>> >>> cecile.madjar at mcin.ca> ??????:
>> >>>
>> >>> Hi Sotirios,
>> >>>
>> >>> The StudyUID is stored in the DicomArchiveID field of the
>> >>> tarchive table. It can also be found in the metadata field but it is
>> mixed
>> >>> with many other information.
>> >>>
>> >>> Hope this helps,
>> >>>
>> >>> C?cile
>> >>>
>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> wrote:
>> >>>
>> >>> Hi,
>> >>>
>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table,
>> >>> specifically at the AcquisitonMetadata column i found something called
>> >>> 'Unique Study ID" in its context, but that must be the Study Instance
>> UID.
>> >>>
>> >>> Thanks
>> >>>
>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar <
>> >>> cecile.madjar at mcin.ca> ??????:
>> >>>
>> >>> Hi Sotirios,
>> >>>
>> >>> Your observation is correct. A little explanation below.
>> >>>
>> >>> MINC files get inserted into the MRI violation tables if:
>> >>>
>> >>> - the scan type could not be identified (not matching an entry in
>> >>> the mri_protocol table)
>> >>> - one parameter of the scan type is out of the expected range
>> >>> present in the mri_protocol_checks (extra filtering in case you
>> need to be
>> >>> stricker on some parameters not present in the mri_protocol table)
>> >>> - if the CandID and PSCID do not match
>> >>>
>> >>> The following cases do not get in the MRI violation tables as it
>> happens
>> >>> before the conversion of the DICOM to MINC files and only MINC files
>> >>> violations are logged there:
>> >>>
>> >>> - "No single DICOM" (since no valid DICOM could be found to convert
>> >>> to MINC)
>> >>> - "Study already inserted" (duplicate StudyUID) since this error
>> >>> happens at the dicomTar.pl level (way before conversion into MINC
>> files)
>> >>>
>> >>> Glad everything is working out!!
>> >>> Best,
>> >>>
>> >>> C?cile
>> >>>
>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> wrote:
>> >>>
>> >>> 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
>> >>>
>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar <
>> >>> cecile.madjar at mcin.ca> ??????:
>> >>>
>> >>> 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!
>> >>>
>> >>> C?cile
>> >>>
>> >>> 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]
>> >>>
>> >>>
>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar <
>> >>> cecile.madjar at mcin.ca> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>>
>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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.
>> >>>
>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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]
>> >>>
>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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]
>> >>>
>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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]
>> >>>
>> >>>
>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs <
>> >>> melanie.legault2 at mcgill.ca> ??????:
>> >>>
>> >>> 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.
>> >>>
>> >>> M?lanie
>> >>>
>> >>> ------------------------------
>> >>> *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
>> >>>
>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs <
>> >>> melanie.legault2 at mcgill.ca> ??????:
>> >>>
>> >>> 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.
>> >>>
>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill
>> >>> University
>> >>> 3801 University, Montr?al, 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
>> >>>
>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> Hi,
>> >>>
>> >>> the parameters in the mri_protocol you have assigned are global
>> >>> standard? or were assigned after trial and error?
>> >>>
>> >>> Thanks
>> >>>
>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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?
>> >>>
>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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? ).
>> >>>
>> >>>
>> >>>
>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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]
>> >>>
>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>>
>> >>>
>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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
>> >>>
>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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.
>> >>>
>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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>>.
>> >>>
>> >>>
>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> 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 $mridir/dicom-archive/.loris_mri/database_config.py
>> >>>
>> >>> Best,
>> >>> Christine
>> >>>
>> >>>
>> >>>
>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> wrote:
>> >>>
>> >>> Hi Christine,
>> >>>
>> >>> If you are referring to the imaging_install.sh here is an image with
>> the
>> >>> configurations i typed. Maybe the problem is somewhere at the last
>> part
>> >>> which asks to configure as much as possible automatically?
>> >>>
>> >>> Thanks
>> >>>
>> >>>
>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. <
>> >>> christine.rogers at mcgill.ca> ??????:
>> >>>
>> >>> Hi Sotirios,
>> >>>
>> >>> Glad to hear your LORIS core install is up and working and all the
>> >>> front-end pages are loading.
>> >>>
>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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]
>> >>>
>> >>>
>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos <
>> >>> sotirisnik at gmail.com> ??????:
>> >>>
>> >>> 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-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>>
>> End of Loris-dev Digest, Vol 64, Issue 16
>> *****************************************
>>
> _______________________________________________
> 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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