[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Wed Nov 13 18:31:43 EST 2019
It's a completely new one vm. The installations steps can be found here
https://github.com/aueb-wim/LORIS-for-MIP and i didn't have installation
issues. Regarding the identical part I checked in the admin panel that the
configurations matched.
Στις Πέμ, 14 Νοε 2019 στις 1:13 π.μ., ο/η Christine Rogers, Ms. <
christine.rogers at mcgill.ca> έγραψε:
> Hi Sotirios -
> Thanks. Before we dive into this over the next few days, can you also let
> us know :
> Was the second machine and/or data partition cloned ? Or else, What's the
> difference between your two installations?
> If it's easy, give us the OS, mariadb version, etc.
> Please also confirm -- did you encounter any installation issues with
> dependency libraries?
> What steps have you taken to verify that the configurations of your
> pipelines, protocol setup, etc are identical in both instances?
> Best,
> Christine
>
> On Wed, Nov 13, 2019 at 5:55 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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>>>>>>
>>>>>> 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
>>>
>>
>
> --
>
> christine.rogers at mcgill.ca
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
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