[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Nov 26 17:17:08 EST 2019
Hi Cecile,
In both my virtual machines
export TMPDIR=/tmp
In both vm also with dcm2mnc i get this output. Just to verify that this
passed in my 1st vm and produced mincs.
I attached the spool as a csv.
[image: image.png]
And also one difference i found was this in the Loris-mri code ( left 1st
workable vm, right 2nd vm that has to be fixed, although i changed it seems
to be independent of the uninitialized value $_ )
[image: image.png]
Thanks,
Sotirios
Στις Τρί, 26 Νοε 2019 στις 11:34 μ.μ., ο/η Cecile Madjar <
cecile.madjar at mcin.ca> έγραψε:
> Hi Sotirios,
>
> that is puzzling... A few additional questions:
>
> - what is the bash variable TMPDIR set to on the environment file?
> - could you try running separately dcm2mnc on the DICOM folder to see
> if that works?
> - could you send us the detailed log from the notification spool table
> (SELECT * FROM notification_spool WHERE UploadID=<your uploadID>) and send
> it back to us? Maybe there are some additional clues that could help
> figuring out what is going on.
>
> Thank you!
>
> Cécile
>
> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> I checked for the StudyInstacueUID at the files with "The target
>> directory does not contain a single DICOM file"" and their attribute has a
>> value.
>>
>> Regarding the scouter and localizer, i modified the settings in the
>> imaging pipeline and now i don't get that error message, but still it
>> doesn't create the mnics.
>>
>> The errors i am getting are ( uninitialized value $_ is not important?
>> because i haven't got comments about that )
>>
>> Use of uninitialized value $_ in pattern match (m//) at
>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>> Running now the following command: /data/loris/data//uploadNeuroDB/
>> imaging_upload_file.pl -profile prod -upload_id 134
>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose
>>
>> and
>>
>> Number of MINC files that will be considered for inserting into the
>> database: 0
>>
>> No data could be converted into valid MINC files.
>>
>> The tarchiveLoader.pl insertion script has failed.
>> Use of uninitialized value $mail_user in concatenation (.) or string at
>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 249.
>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 250.
>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>> batch_uploads_imageuploader.pl line 251.
>>
>> Thanks
>>
>> Sotirios
>>
>> Στις Δευ, 25 Νοε 2019 στις 5:22 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> 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
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>>>>>>>>>>>>
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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
>>>>>>>>>>>> >>>
>>>>>>>>>>>> >>>
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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
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>>>>>>>>>>>>
>>>>>>>>>>>> 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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