[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Nov 26 10:12:37 EST 2019
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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>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Today's Topics:
>>>>>>>>>>
>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>> Message: 1
>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>> From: Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>> Message-ID:
>>>>>>>>>> <CAKHj7uST=
>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com>
>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to
>>>>>>>>>> diagnose the
>>>>>>>>>> warnings we get?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>
>>>>>>>>>> > Hi Cecile,
>>>>>>>>>> >
>>>>>>>>>> > We were wondering whether Loris has a tool to check if there
>>>>>>>>>> are problems
>>>>>>>>>> > with the dcm files, before trying to upload them. Something
>>>>>>>>>> that could
>>>>>>>>>> > provide the same results provided in the warning_output, this
>>>>>>>>>> is the
>>>>>>>>>> > summary from the mri_upload at the front-page. Also which
>>>>>>>>>> attributes of the
>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file header
>>>>>>>>>> > specification for Loris?
>>>>>>>>>> >
>>>>>>>>>> > Thanks
>>>>>>>>>> >
>>>>>>>>>> > Sotirios
>>>>>>>>>> >
>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>> >
>>>>>>>>>> >> Hi,
>>>>>>>>>> >>
>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it
>>>>>>>>>> worked,but i
>>>>>>>>>> >> thought that something else was causing the 2nd issue.
>>>>>>>>>> >> Thanks
>>>>>>>>>> >>
>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, <
>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>> >>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and
>>>>>>>>>> columns are of
>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be
>>>>>>>>>> using
>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>> >>>
>>>>>>>>>> >>> The second error occurs because the trigger triggers a
>>>>>>>>>> rollback of the
>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>> >>> See mysql documentation for trigger error handling.
>>>>>>>>>> >>>
>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in
>>>>>>>>>> failure of
>>>>>>>>>> >>> the entire statement that caused trigger invocation.
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>> >>> -- Xavier
>>>>>>>>>> >>>
>>>>>>>>>> >>> ------------------------------
>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios
>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>> >>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>> >>>
>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the file
>>>>>>>>>> table are
>>>>>>>>>> >>> inserted too
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as well,
>>>>>>>>>> because i
>>>>>>>>>> >>> don't want manually to label them as passed throught the
>>>>>>>>>> interface
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>> >>>
>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>> >>> BEGIN
>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID,
>>>>>>>>>> >>> EchoTime = NEW.EchoTime,
>>>>>>>>>> >>> QCStatus = "Pass",
>>>>>>>>>> >>> QCFirstChangeTime = NOW(),
>>>>>>>>>> >>> QCLastChangeTime = NOW();
>>>>>>>>>> >>> END
>>>>>>>>>> >>>
>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>> >>>
>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column
>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a
>>>>>>>>>> foreign
>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES
>>>>>>>>>> `files` (`FileID`))
>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column
>>>>>>>>>> associated with
>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it
>>>>>>>>>> means no DICOMs
>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the
>>>>>>>>>> insertion of the
>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with the
>>>>>>>>>> correct
>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to
>>>>>>>>>> the files
>>>>>>>>>> >>> table (hence, the MINC files). You could always create a new
>>>>>>>>>> table for
>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table?
>>>>>>>>>> >>>
>>>>>>>>>> >>> C?cile
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all their
>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of creating
>>>>>>>>>> a trigger for
>>>>>>>>>> >>> that, but which tables do i need to add entries to? So far
>>>>>>>>>> from what i see
>>>>>>>>>> >>> i need to add entres at the table "files" whenever an
>>>>>>>>>> insertion happens to
>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning
>>>>>>>>>> of my email
>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the
>>>>>>>>>> StudyID i am
>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks.
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the
>>>>>>>>>> >>> tarchive table. It can also be found in the metadata field
>>>>>>>>>> but it is mixed
>>>>>>>>>> >>> with many other information.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>> >>>
>>>>>>>>>> >>> C?cile
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive
>>>>>>>>>> table,
>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found
>>>>>>>>>> something called
>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study
>>>>>>>>>> Instance UID.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Your observation is correct. A little explanation below.
>>>>>>>>>> >>>
>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if:
>>>>>>>>>> >>>
>>>>>>>>>> >>> - the scan type could not be identified (not matching an
>>>>>>>>>> entry in
>>>>>>>>>> >>> the mri_protocol table)
>>>>>>>>>> >>> - one parameter of the scan type is out of the expected
>>>>>>>>>> range
>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in
>>>>>>>>>> case you need to be
>>>>>>>>>> >>> stricker on some parameters not present in the
>>>>>>>>>> mri_protocol table)
>>>>>>>>>> >>> - if the CandID and PSCID do not match
>>>>>>>>>> >>>
>>>>>>>>>> >>> The following cases do not get in the MRI violation tables as
>>>>>>>>>> it happens
>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only
>>>>>>>>>> MINC files
>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>> >>>
>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found
>>>>>>>>>> to convert
>>>>>>>>>> >>> to MINC)
>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this
>>>>>>>>>> error
>>>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion
>>>>>>>>>> into MINC files)
>>>>>>>>>> >>>
>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>>
>>>>>>>>>> >>> C?cile
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram.
>>>>>>>>>> Now about the
>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there
>>>>>>>>>> only if there is
>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header
>>>>>>>>>> parameter?
>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with
>>>>>>>>>> the 2 studyiuid
>>>>>>>>>> >>> to be there.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I think
>>>>>>>>>> most of our
>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>> >>>
>>>>>>>>>> >>> C?cile
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> about that dicom that had that insertion error it's about
>>>>>>>>>> 30mb and when
>>>>>>>>>> >>> it is being processed the ram is being drastically increased
>>>>>>>>>> from 2gb to
>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is
>>>>>>>>>> the recommended
>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>> >>>
>>>>>>>>>> >>> For the delete script issue, if you are absolutely certain
>>>>>>>>>> that no
>>>>>>>>>> >>> processes are run for that uploadID, you can update the
>>>>>>>>>> mri_upload table
>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that
>>>>>>>>>> uploadID. It
>>>>>>>>>> >>> looks like for some reason the scripts did not update this
>>>>>>>>>> field when it
>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the case
>>>>>>>>>> though.
>>>>>>>>>> >>> Note: only do that update if you are certain that there is no
>>>>>>>>>> processing
>>>>>>>>>> >>> happening.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they
>>>>>>>>>> actually do
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> I thought that this might be a permission because "w" was
>>>>>>>>>> missing at the
>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but
>>>>>>>>>> with no mnic
>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>> >>>
>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently
>>>>>>>>>> processing it.
>>>>>>>>>> >>>
>>>>>>>>>> >>> How can solve this?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>> >>>
>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header
>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max,
>>>>>>>>>> TE_min,
>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the
>>>>>>>>>> mri_protocol table
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>> >>>
>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation "T1
>>>>>>>>>> AXIAL SE
>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i
>>>>>>>>>> find that weird
>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>> >>>
>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does
>>>>>>>>>> not contain a
>>>>>>>>>> >>> single DICOM file.", therefore they are missing their StudyUID
>>>>>>>>>> >>>
>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from
>>>>>>>>>> multiple
>>>>>>>>>> >>> studies."
>>>>>>>>>> >>>
>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC
>>>>>>>>>> files.
>>>>>>>>>> >>> localizer, scout will not be considered!" What is this?
>>>>>>>>>> >>>
>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579
>>>>>>>>>> and 102506134
>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thank you,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Sotirios
>>>>>>>>>> >>>
>>>>>>>>>> >>> PS
>>>>>>>>>> >>>
>>>>>>>>>> >>> To diagnose a folder search the name of the folder at
>>>>>>>>>> dicom_output.txt.
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully
>>>>>>>>>> documented here
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>> >
>>>>>>>>>> >>> -- let us know if you didn't find the answers you were
>>>>>>>>>> looking for there.
>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your
>>>>>>>>>> database
>>>>>>>>>> >>> management software is a visual placeholder for you as the
>>>>>>>>>> user? I'm not
>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as
>>>>>>>>>> your screenshot
>>>>>>>>>> >>> showed.)
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> I tried to create a new candidate using the API, is there
>>>>>>>>>> something
>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal
>>>>>>>>>> error? In the
>>>>>>>>>> >>> loris-error log it state that there is something wrong with
>>>>>>>>>> token, but i
>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>> >>>
>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535]
>>>>>>>>>> [client
>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError:
>>>>>>>>>> Argument 1
>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the
>>>>>>>>>> type string,
>>>>>>>>>> >>> null given, called in
>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on
>>>>>>>>>> line 169 and
>>>>>>>>>> >>> defined in
>>>>>>>>>> >>>
>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5
>>>>>>>>>> {main}\n thrown in
>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on
>>>>>>>>>> line 192
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you
>>>>>>>>>> know what i
>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed
>>>>>>>>>> dependencies.
>>>>>>>>>> >>>
>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way
>>>>>>>>>> to omit
>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>> >>>
>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all
>>>>>>>>>> the entries
>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry
>>>>>>>>>> with the 0 ID.
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> We recommend that you use our existing tools for creating new
>>>>>>>>>> candidates
>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by
>>>>>>>>>> calling the Candidate
>>>>>>>>>> >>> class's createNew()
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>> >function.
>>>>>>>>>> >>> These will create the necessary records for you. (It's not
>>>>>>>>>> recommended to
>>>>>>>>>> >>> make direct modifications to mysql database tables in your
>>>>>>>>>> script, if I
>>>>>>>>>> >>> understand you.)
>>>>>>>>>> >>>
>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and
>>>>>>>>>> there are
>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the
>>>>>>>>>> External ID field
>>>>>>>>>> >>> in the candidate table can also be used for any values you
>>>>>>>>>> like.
>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in
>>>>>>>>>> parallel - these
>>>>>>>>>> >>> are entered/visible in the Candidate Information module and
>>>>>>>>>> added in the
>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> We are building a script that will auto insert the candidates
>>>>>>>>>> based on
>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we are
>>>>>>>>>> creating a new
>>>>>>>>>> >>> profile in the candidate table, if we also have to insert a
>>>>>>>>>> new record at
>>>>>>>>>> >>> another table? Furthermore is there a problem that in our
>>>>>>>>>> case CandID won't
>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault,
>>>>>>>>>> Mrs <
>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> That would normally be the case but the numeric part of the
>>>>>>>>>> PSCID get
>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4
>>>>>>>>>> numerical char
>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>> >>>
>>>>>>>>>> >>> ABC0001
>>>>>>>>>> >>> ABC0002
>>>>>>>>>> >>> ...
>>>>>>>>>> >>> ABC0010
>>>>>>>>>> >>> ...
>>>>>>>>>> >>>
>>>>>>>>>> >>> thus sorting them ascending will always get the latest value
>>>>>>>>>> generated
>>>>>>>>>> >>> as the max value.
>>>>>>>>>> >>>
>>>>>>>>>> >>> M?lanie
>>>>>>>>>> >>>
>>>>>>>>>> >>> ------------------------------
>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>> >>>
>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be
>>>>>>>>>> stored
>>>>>>>>>> >>> within a specific length of characters. Otherwise if we were
>>>>>>>>>> to sort
>>>>>>>>>> >>> strings with different lengths the result would not be sorted
>>>>>>>>>> correctly (
>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault,
>>>>>>>>>> Mrs <
>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>> >>> The code simply look for the PSCID with the max value and
>>>>>>>>>> increase that
>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>> >>>
>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine |
>>>>>>>>>> McGill
>>>>>>>>>> >>> University
>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>> >>>
>>>>>>>>>> >>> ------------------------------
>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios
>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> how does Loris determine the next available PSCID value for a
>>>>>>>>>> new
>>>>>>>>>> >>> candidate?
>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where do
>>>>>>>>>> we store the
>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are
>>>>>>>>>> global
>>>>>>>>>> >>> standard? or were assigned after trial and error?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Given you have done the initial setup of your tables to match
>>>>>>>>>> your
>>>>>>>>>> >>> intended protocol/parameters according to instructions --
>>>>>>>>>> >>> the Troubleshooting guide documentation recommends
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>> >
>>>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads).
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> *if i were to change their status to resolve what would
>>>>>>>>>> happen?
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from
>>>>>>>>>> the
>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>> >>> if i were to click their issue to resolve what would happend?
>>>>>>>>>> would they
>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> The defaut values of the schema exists in my local database.
>>>>>>>>>> If i adjust
>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be
>>>>>>>>>> uploaded?
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol
>>>>>>>>>> table ? (and
>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans)
>>>>>>>>>> >>>
>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging
>>>>>>>>>> insertion
>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>> >>>
>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You can
>>>>>>>>>> adapt the
>>>>>>>>>> >>> insert statements which load the default table values -->
>>>>>>>>>> e.g. Here on
>>>>>>>>>> >>> GitHub :
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> I see that i can edit the values but not how to insert new
>>>>>>>>>> rows.
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be inserted?
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>> >>>
>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough.
>>>>>>>>>> >>>
>>>>>>>>>> >>> It says "could not identify scan type", which we knew
>>>>>>>>>> already. Did you
>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>> >>>
>>>>>>>>>> >>> It will take you to the next page of the module, showing for
>>>>>>>>>> each scan
>>>>>>>>>> >>> what the scan parameters were, and will also show for
>>>>>>>>>> comparison what's
>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>> >>> Compare these values to find which parameter was not correct
>>>>>>>>>> according
>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions.
>>>>>>>>>> >>>
>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges
>>>>>>>>>> (e.g. TR, TE)
>>>>>>>>>> >>> for scans.
>>>>>>>>>> >>> This can be done in the front-end, by editing the database
>>>>>>>>>> table
>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module.
>>>>>>>>>> >>>
>>>>>>>>>> >>> The MRI Violations module features are explained in more
>>>>>>>>>> detail in the
>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon
>>>>>>>>>> in the menu
>>>>>>>>>> >>> bar.)
>>>>>>>>>> >>>
>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>> >
>>>>>>>>>> >>> : no MINCs inserted- violated scans
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> looks like my previous email's attachment wasn't delivered
>>>>>>>>>> due to
>>>>>>>>>> >>> security reasons, i uploaded my file at google drive
>>>>>>>>>> >>>
>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> For the mri_violations i attached the .html output from
>>>>>>>>>> webbrowser, so
>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>> >>>
>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're getting
>>>>>>>>>> an Endian
>>>>>>>>>> >>> warning. (it's a warning not an error, correct?)
>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all
>>>>>>>>>> successfully
>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>> >>>
>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your
>>>>>>>>>> dcmodify command is
>>>>>>>>>> >>> a great and fast solution for bulk header updates.
>>>>>>>>>> >>>
>>>>>>>>>> >>> If you're concerned about fields being changed (e.g.
>>>>>>>>>> "(2001,105f)" from
>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice
>>>>>>>>>> before and look
>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS
>>>>>>>>>> before/after
>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff the
>>>>>>>>>> outputs --
>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not
>>>>>>>>>> recognized or
>>>>>>>>>> >>> unknown : this means your scans did not match what is
>>>>>>>>>> stored in your
>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see why
>>>>>>>>>> they didn't
>>>>>>>>>> >>> match?
>>>>>>>>>> >>> Send us an example, in addition to the contents of the
>>>>>>>>>> mri_protocol
>>>>>>>>>> >>> table, if you can't find the source of the mismatch.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Here is the psc table
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> I created 2 candidates profiles through the interface
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>> >>>
>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>> >>>
>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length,
>>>>>>>>>> reading a
>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>> >>>
>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can
>>>>>>>>>> see the
>>>>>>>>>> >>> execution for the second dicom. Mnics could not be inserted
>>>>>>>>>> due to
>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12
>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>> >>>
>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name
>>>>>>>>>> '__MACOSX'
>>>>>>>>>> >>> -delete
>>>>>>>>>> >>>
>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod
>>>>>>>>>> -verbose
>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>> >>>
>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>> >>> Database is available.
>>>>>>>>>> >>>
>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>>>>>>> >>>
>>>>>>>>>> >>> You are creating a tar with the following command:
>>>>>>>>>> >>>
>>>>>>>>>> >>> tar -cf
>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>> >>>
>>>>>>>>>> >>> * Taken from dir :
>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>> >>> * Archive target location :
>>>>>>>>>> >>>
>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>> >>> * Name of creating host : 127.0.1.1
>>>>>>>>>> >>> * Name of host OS : Linux
>>>>>>>>>> >>> * Created by user : lorisadmin
>>>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50
>>>>>>>>>> >>> * dicomSummary version : 1
>>>>>>>>>> >>> * dicomTar version : 1
>>>>>>>>>> >>> * md5sum for DICOM tarball :
>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>> >>> * md5sum for complete archive :
>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>> >>>
>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>> >>>
>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>> >>>
>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl
>>>>>>>>>> -globLocation
>>>>>>>>>> >>> -profile prod
>>>>>>>>>> >>>
>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>> >>> md5sum
>>>>>>>>>> >>>
>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>>
>>>>>>>>>> >>> Number of MINC files that will be considered for inserting
>>>>>>>>>> into the
>>>>>>>>>> >>> database: 2
>>>>>>>>>> >>>
>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>> >>>
>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>> >>>
>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>> >>>
>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>> cat
>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>> >>>
>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>> >>>
>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>> >>>
>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>> >>>
>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>> >>>
>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>> >>>
>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>> >>>
>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>> >>>
>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>> >>>
>>>>>>>>>> >>> --> The minc file cannot be registered since the
>>>>>>>>>> AcquisitionProtocol
>>>>>>>>>> >>> is unknown
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the
>>>>>>>>>> *delete_imaging_upload*
>>>>>>>>>> >>> script --
>>>>>>>>>> >>> details here:
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>> >>>
>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? This
>>>>>>>>>> is a
>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>> >
>>>>>>>>>> >>> )
>>>>>>>>>> >>> The foreign key constraint error on the candidate record is
>>>>>>>>>> curious.
>>>>>>>>>> >>>
>>>>>>>>>> >>> There are also a few options for creating candidates when
>>>>>>>>>> inserting
>>>>>>>>>> >>> imaging data:
>>>>>>>>>> >>>
>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion
>>>>>>>>>> pipeline
>>>>>>>>>> >>>
>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits,
>>>>>>>>>> optionally I
>>>>>>>>>> >>> think)
>>>>>>>>>> >>> How to:
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>> >
>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>> >>> You will want to first ensure that the PatientName header in
>>>>>>>>>> the DICOMs
>>>>>>>>>> >>> as well as tar package are correctly labelled with
>>>>>>>>>> PSCID_DCCID_VisitLabel
>>>>>>>>>> >>>
>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>> >>> How to :
>>>>>>>>>> >>>
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>> >>>
>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the
>>>>>>>>>> bids_import script,
>>>>>>>>>> >>> to automatically create your candidates and sessions.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to create a
>>>>>>>>>> new
>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>> >>>
>>>>>>>>>> >>> *First execution:*
>>>>>>>>>> >>>
>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>> ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>> >>> log.txt
>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a
>>>>>>>>>> foreign
>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT
>>>>>>>>>> `FK_candidate_1`
>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>>>>>>>>> (`CenterID`)) at
>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner:
>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES
>>>>>>>>>> (?,?,?,?,?)';
>>>>>>>>>> >>> SET
>>>>>>>>>> >>>
>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key
>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT
>>>>>>>>>> `FK_mri_scanner_1`
>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`))
>>>>>>>>>> (error code 1452)
>>>>>>>>>> >>>
>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the
>>>>>>>>>> validation again
>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force
>>>>>>>>>> to force the
>>>>>>>>>> >>> execution.
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>> >>> line 250.
>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>> >>> line 251.
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>> >>>
>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>> ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>> >>> log.txt
>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>> >>>
>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study.
>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>> >>> This is the information retained from the first time the
>>>>>>>>>> study was
>>>>>>>>>> >>> inserted:
>>>>>>>>>> >>>
>>>>>>>>>> >>> * Taken from dir :
>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>> >>> * Archive target location :
>>>>>>>>>> >>>
>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>> >>> * Name of creating host : 127.0.1.1
>>>>>>>>>> >>> * Name of host OS : Linux
>>>>>>>>>> >>> * Created by user : lorisadmin
>>>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05
>>>>>>>>>> >>> * dicomSummary version : 1
>>>>>>>>>> >>> * dicomTar version : 1
>>>>>>>>>> >>> * md5sum for DICOM tarball :
>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>> >>> * md5sum for complete archive :
>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> Last update of record:
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>> >>> line 250.
>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>> >>> line 251.
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you
>>>>>>>>>> next encounter
>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup docs
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>.
>>>>>>>>>> >>> I'll look into how we can better handle the incoming/
>>>>>>>>>> directory next
>>>>>>>>>> >>> time.
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. Also
>>>>>>>>>> i have tested
>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>> >>>
>>>>>>>>>> >>> I executed the script again, because the only error i had
>>>>>>>>>> previously was
>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are no
>>>>>>>>>> errors
>>>>>>>>>> >>> reported back except of warnings <<mysql: [Warning] Using a
>>>>>>>>>> password on the
>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> It's possible -- if the script was unable to connect to the
>>>>>>>>>> database
>>>>>>>>>> >>> during its execution (e.g. typo in the password), that would
>>>>>>>>>> explain the
>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in
>>>>>>>>>> the Config
>>>>>>>>>> >>> module.
>>>>>>>>>> >>> It's hard to tell without seeing the output from your script
>>>>>>>>>> run -- Did
>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh
>>>>>>>>>> script (starting
>>>>>>>>>> >>> at line 222
>>>>>>>>>> >>> <
>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>> >
>>>>>>>>>> >>> )
>>>>>>>>>> >>>
>>>>>>>>>> >>> For example, check if the database connection information was
>>>>>>>>>> populated
>>>>>>>>>> >>> accurately in
>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>> >>>
>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an
>>>>>>>>>> image with the
>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at the
>>>>>>>>>> last part
>>>>>>>>>> >>> which asks to configure as much as possible automatically?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers,
>>>>>>>>>> Ms. <
>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>> >>>
>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working and
>>>>>>>>>> all the
>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>> >>>
>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775
>>>>>>>>>> project
>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and
>>>>>>>>>> that
>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the
>>>>>>>>>> install
>>>>>>>>>> >>> Readme <https://github.com/aces/Loris#install-steps>.
>>>>>>>>>> >>>
>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change
>>>>>>>>>> LORIS to
>>>>>>>>>> >>> loris, right?
>>>>>>>>>> >>>
>>>>>>>>>> >>> These imaging paths will be updated during your imaging
>>>>>>>>>> installation
>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by an automated
>>>>>>>>>> script --
>>>>>>>>>> >>> you do not need to set them manually via the Config module.
>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for detailed
>>>>>>>>>> steps to follow.
>>>>>>>>>> >>>
>>>>>>>>>> >>> Best,
>>>>>>>>>> >>> Christine
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>> >>>
>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change
>>>>>>>>>> LORIS to loris,
>>>>>>>>>> >>> right?
>>>>>>>>>> >>>
>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios
>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>> >>>
>>>>>>>>>> >>> Hi,
>>>>>>>>>> >>>
>>>>>>>>>> >>> i used
>>>>>>>>>> >>>
>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash
>>>>>>>>>> -
>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> you had suggested in the past, make worked and now i can see
>>>>>>>>>> all the
>>>>>>>>>> >>> contents in the web-interface, but i don't need make install?
>>>>>>>>>> >>>
>>>>>>>>>> >>> Thanks
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> >>> --
>>>>>>>>>> >>>
>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>> >>>
>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>> >>>
>>>>>>>>>> >>>
>>>>>>>>>> -------------- next part --------------
>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>> URL: <
>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>> >
>>>>>>>>>>
>>>>>>>>>> ------------------------------
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>> *****************************************
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Loris-dev mailing list
>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Loris-dev mailing list
>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> christine.rogers at mcgill.ca
>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>> Montreal Neurological Institute
>>>>>>> McGill University | Montreal | Canada
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Loris-dev mailing list
>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>
>>>>>
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