[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Nov 25 09:58:04 EST 2019
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
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>>>>>>>>
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>>>>>>>>
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>>>>>>>>
>>>>>>>> When replying, please edit your Subject line so it is more specific
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>>>>>>>>
>>>>>>>>
>>>>>>>> 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
>>>>>>>> >>>
>>>>>>>> >>>
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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
>>>>>>>
>>>>>> _______________________________________________
>>>>>> 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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