[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Sep 30 08:55:44 EDT 2019
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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