[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Oct 1 06:55:31 EDT 2019
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
Στις Δευ, 30 Σεπ 2019 στις 4:04 μ.μ., ο/η Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> έγραψε:
> Oh, sorry i should have asked for StudyID, at the beginning of my email i
> sent 3 hours ago (not StudyUID).
>
> Στις Δευ, 30 Σεπ 2019 στις 3:55 μ.μ., ο/η Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> έγραψε:
>
>> 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.
>>
>> Στις Δευ, 30 Σεπ 2019 στις 3:38 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> 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,
>>>
>>> Cécile
>>>
>>> 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
>>>>
>>>> Στις Παρ, 27 Σεπ 2019 στις 4:22 μ.μ., ο/η Cecile Madjar <
>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>
>>>>> 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,
>>>>>
>>>>> Cécile
>>>>>
>>>>> 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
>>>>>>
>>>>>> Στις Πέμ, 26 Σεπ 2019 στις 5:07 μ.μ., ο/η Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>
>>>>>>> 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!
>>>>>>>
>>>>>>> Cécile
>>>>>>>
>>>>>>> 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]
>>>>>>>>
>>>>>>>>
>>>>>>>> Στις Τρί, 24 Σεπ 2019 στις 11:24 μ.μ., ο/η Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 24 Σεπ 2019 στις 2:30 π.μ., ο/η Sotirios
>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> 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.
>>>>>>>>>>>
>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 4:54 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>>> 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]
>>>>>>>>>>>>>
>>>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 4:37 μ.μ., ο/η Sotirios
>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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]
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault,
>>>>>>>>>>>>>>>>> Mrs <melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Mélanie
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>> *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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie
>>>>>>>>>>>>>>>>>> Legault, Mrs <melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Mélanie Legault | Software developer | Faculty of
>>>>>>>>>>>>>>>>>> Medicine | McGill University
>>>>>>>>>>>>>>>>>> 3801 University, Montréal, 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> the parameters in the mri_protocol you have assigned are
>>>>>>>>>>>>>>>>>> global standard? or were assigned after trial and error?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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? ).
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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>>.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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 $mridir
>>>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an
>>>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at
>>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working
>>>>>>>>>>>>>>>>>> and all the front-end pages are loading.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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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