[Loris-dev] Import mri - scripts
Cecile Madjar
cecile.madjar at mcin.ca
Mon Nov 25 10:22:26 EST 2019
Hi Sotirios,
OK. So the issue I mentioned should not be a problem for you.
Is the StudyInstanceUID DICOM header set in your images? If it is not set,
then you would end up with the error message "The target directory does not
contain a single DICOM file". So maybe this is the issue you are having
with those datasets?
Regarding not excluding series descriptions, you can configure that in the
Config module under the Imaging Pipeline section. Simply remove all entries
for the "Series description to exclude from imaging insertion" setting.
Cécile
On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> Hi Cecile,
>
> We are using this version
> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to
> insert low resolution now?
>
> Thanks
>
> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <cecile.madjar at mcin.ca> wrote:
>
>> Hi Sotirios,
>>
>> Which version of LORIS-MRI are you using?
>>
>> There was a bug that got resolved in 20.2 in get_dicom_info.pl.
>> Basically, if a DICOM did not have the (0020,0032) header,
>> get_dicom_info.pl considered that the file was not a DICOM, which was a
>> mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is the
>> issue you are encountering.
>>
>> About scout and localizer, they are a type of short and low resolution
>> sequence that is used by the tech but is of no interest scientifically,
>> which is why we tend to no insert them.
>>
>> Hope this helps,
>>
>> Cécile
>>
>>
>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Cecile,
>>>
>>> i executed the find command and the output i got per folder was "DICOM
>>> medical imaging data. Maybe there is something wrong with the find command
>>> in the warning that it is unable to check if the file is a dicom file? Also
>>> when i use get_dicom_info.pl i don't get any output data. Finally i
>>> don't understand what scout or localizer is ( something like if and only if
>>> a file fails then the whole session is invalid? ).
>>>
>>> [image: image.png]
>>>
>>> Thanks
>>>
>>> Sotirios
>>>
>>> Στις Τρί, 19 Νοε 2019 στις 9:40 μ.μ., ο/η Cecile Madjar <
>>> cecile.madjar at mcin.ca> έγραψε:
>>>
>>>> Hi Sotirios,
>>>>
>>>> I took a closer look to the batch_uploader_multiple_output.txt file you
>>>> sent. It looks like there are different reasons for failure depending on
>>>> the DICOM folder uploaded.
>>>>
>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1:
>>>> it looks like there is no file of type DICOM in the folder. Have you
>>>> checked to see if that is indeed the case? Maybe you can try running the
>>>> following command on that folder to see what are the types of the files? If
>>>> it does not return at least one DICOM medical imaging data file, then that
>>>> is why you get the error message from the pipeline:
>>>> -
>>>>
>>>> find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>
>>>> - For 864173 DCC0001 V1: it looks like there are two different
>>>> DICOM studies within the same folder. You will need to split that study in
>>>> two based on the StudyUID field as the insertion pipeline does not allow
>>>> for more than one StudyUID per upload.
>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1:
>>>> it looks like the dcm2mnc command did not produce any MINC files. Can you
>>>> check in the DICOM archive what are the series present in the tarchive for
>>>> that visit? Maybe only a scout or localizer was acquired for that session,
>>>> hence the no valid MINC files (scout and localizer being skipped for the
>>>> conversion)
>>>> - For 397410 DCC0003 V1: it looks like everything went well for
>>>> this one.
>>>>
>>>> One script that is called by our pipeline is called get_dicom_info.pl and
>>>> this does all kind of checks on the DICOM files (it is being called when
>>>> running the dcm2mnc conversion). You could run it independently on your
>>>> folder if needed.
>>>>
>>>> Since one of the study got in, it does not look like you are having a
>>>> problem with the setup. It seems more likely to be a problem with the data
>>>> themselves.
>>>>
>>>> Hope this helps.
>>>>
>>>> Cécile
>>>>
>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi Christine,
>>>>>
>>>>> In my first vm i am able to create the minc files and view them at the
>>>>> mri browser (except of candidate 102761034 ), meanwhile the same files
>>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen
>>>>> in the file attached.
>>>>> Also a colleague of us has built a pre-validation tool for dicom
>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had found
>>>>> all the files that Loris gave as warning . Basically I confirmed that the
>>>>> total amount of files per dicom was the same amount as stated in Loris and
>>>>> checked some filenames given from warning to confirm that they match with
>>>>> our tool. But that was months ago and my colleague had changed some
>>>>> parameters for MIP and now our tool doesn't find all the invalid files,
>>>>> that's why i asked for the dicom header specification of Loris. In a
>>>>> discussion we had he mentioned that he doesn't check for some tags e.x.
>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to
>>>>> remove invalid dcm files.
>>>>>
>>>>> Thanks
>>>>>
>>>>> Στις Τετ, 13 Νοε 2019 στις 11:45 μ.μ., ο/η Christine Rogers, Ms. <
>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>
>>>>>> Hi Sotirios,
>>>>>> Can you provide us with some fresh particulars of the current issue
>>>>>> and we'll take it from there?
>>>>>> Yang's team has built these scripts which can definitely serve as a
>>>>>> model for your pre-validation of your DICOM collections.
>>>>>> cheers,
>>>>>> Christine
>>>>>>
>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> 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:
>>>>>>>>
>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>> loris-dev at bic.mni.mcgill.ca
>>>>>>>>>
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>>>>>>>>> When replying, please edit your Subject line so it is more specific
>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Today's Topics:
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>>> >>>
>>>>>>>>> >>>
>>>>>>>>> -------------- next part --------------
>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>> URL: <
>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>> >
>>>>>>>>>
>>>>>>>>> ------------------------------
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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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