[Loris-dev] Import mri - scripts
Cecile Madjar
cecile.madjar at mcin.ca
Mon Sep 30 09:04:12 EDT 2019
Ooops, sorry. I read to quickly... You are right. It does not look like we
are storing that information at the DICOM level.
However, you can see that information in the parameter_file table once the
MINC file has been inserted into the database using the following query:
SELECT File, Name, Value FROM files JOIN parameter_file USING (FileID) JOIN
parameter_type USING (ParameterTypeID) WHERE Name='study:study_id';
Hope this helps and sorry again for the confusion...
Cécile
On Mon, Sep 30, 2019 at 8:56 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> 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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