[Loris-dev] Import mri - scripts
Christine Rogers, Ms.
christine.rogers at mcgill.ca
Thu Aug 29 09:04:30 EDT 2019
Hi Sotirios,
> Any suggestion why Loris is not showing up in the browser?
- What are the last few lines of your loris-access and loris-error apache logs?
- What are the URL and host in your Config table? (run these queries from the wiki<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>)
- Are you using https, are the certificates in place, etc?
- Do any of the wiki's Troubleshooting steps<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> help?
Best,
Christine
On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Any suggestion why Loris is not showing up in the browser?
Thanks
Στις Τετ, 28 Αυγ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Also to mention that in the picture i opened the 000-default.conf which is just a copy of loris.conf by using cp
Στις Τετ, 28 Αυγ 2019 στις 2:20 π.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Ok that fixed the install.sh problem. Now it doesn't show loris to the browser, although everything seems right ( also
/etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ).
And apache is running
lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status apache2[sudo] password for lorisadmin:
● apache2.service - LSB: Apache2 web server
Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
Drop-In: /lib/systemd/system/apache2.service.d
└─apache2-systemd.conf
Active: active (running) since Τετ 2019-08-28 02:15:12 EEST; 3min 34s ago
[image.png]
Στις Τρί, 27 Αυγ 2019 στις 9:42 μ.μ., ο/η Shen Wang <wangshen.mcin at gmail.com<mailto:wangshen.mcin at gmail.com>> έγραψε:
Hi,
This is a bug for install.sh file, we will fix it later.
Thank for letting me know your Loris install situation.
regards
Shen
On Tue, 27 Aug 2019 at 14:28, Shen Wang <wangshen.mcin at gmail.com<mailto:wangshen.mcin at gmail.com>> wrote:
Hi,
Please remove "set -euo pipefail" line 10 in the install.sh file.
Then try again.
On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi,
i still haven't resolved the previous issue. Also i tried to install Loris to a new virtual machine and when i execute install.sh i get the following error
lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh
LORIS Installation Script starting at 2019-08-27T21:00:42
The log for this session will be stored in file /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log
---------------------------------------------------------------------
LORIS Installation Script
---------------------------------------------------------------------
PHP appears to be installed.
PHP Composer appears to be installed.
This install script will ask you to provide inputs for different steps.
Please ensure you have the following information ready (if applicable):
1) Your project directory name.
(Will be used to modify the paths for Imaging data in the generated
config.xml file for LORIS, and may also be used to automatically
create/install apache config files.) If unsure, a default like "LORIS"
should be acceptable.
Please also consult the Loris WIKI on GitHub for more information on these
Install Script input parameters.
Ready to continue? [yn] y
./install.sh: line 132: projectname: unbound variable
Thanks
Στις Τρί, 6 Αυγ 2019 στις 5:09 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,
Could you also let us know -- on which pages is content visible, and on which pages/modules is content not visible for you?
Thanks,
Christine
On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
Thanks Sotirios,
That's good to know. It sounds like you've checked that your /var/www/loris/project/config.xml file get populated properly.
Please send us the last few errors you're seeing in your apache error log file, and your config paths and we can see what's happening with your front end --
Run these Troubleshooting Queries<https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings> to get your config path settings, given your front end is not displaying fully.
The Loris-MRI repo<https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21 install/upgrade would then be your next steps.
Best,
Christine
On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
I am using a VM. What i did was:
1) Download the files from https://github.com/aces/Loris and replace them to my existing /vaw/www/loris folder.
2) Execute the composer install --no-dev and then composer dump-autoload as mentioned here https://github.com/aces/Loris/wiki/Updating-your-LORIS.
3) Execute install.sh from /var/www/loris/tools and because LORIS already existed i moved a .config file, then re-executed the install.sh successfully
4 ) As for the database, i dropped the schema and i executed the installdb.php
Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotorios,
Thanks - when you re-installed did you start on a fresh root path / VM or might some of your old system setting still apply?
(And if you did any steps similar to an upgrade, did you follow the Upgrade steps in the Release Notes, from both repos?)
About the TR_range column - it was recently split (MRI pr339<https://github.com/aces/Loris-MRI/pull/339>) split into TR_min and _max columns. Given the code was trying to query TR_range which does not exist in your mri_protocol table, double-check which version of the Loris repo (tables) and the Loris-MRI repo (code) you have installed to ensure they match.
Christine
On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
I reinstalled LORIS to 21 version and now the content is not visible at all at most pages.
[image.png]
Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Hi,
Is it easy to upgrade to Loris 21? Also the following fails because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol which doesn't have TR_range https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
[image.png]
lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147.
base is DCC0000_258024_V1
path is /data/incoming/
type is .tar.gz
fullpath is /data/incoming/DCC0000_258024_V1.tar.gz
DBD::mysql::st execute failed: Unknown column 'TR_range' in 'where clause' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
DBD::mysql::st fetchrow_array failed: fetch() without execute() at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1986.
Use of uninitialized value $count_mri_protocol in numeric gt (>) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1995.
DBD::mysql::st execute failed: Unknown column 'TR_range' in 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562.
Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
No Mincs inserted
Thanks,
Sotirios
Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,
First, just a note: we've released LORIS 21 this week with some major new features and cleanup -- especially if you are early in your setup phase, check out the Release notes for both the LORIS<https://github.com/aces/Loris/releases/tag/v21.0.0> and Loris-MRI<https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> repos.
Thanks for your screenshots -- your empty mri_protocol table should be at the root of these issues :
The mri_protocol table must be populated<https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database> in order for your scans to be registered in LORIS -- it serves as a whitelist for the insertion pipeline which filters out scans that aren't identified or matched to scan types in this table.
By default, this table is populated with entries for t1, t2, fMRI and DTI (Insert statements for 21 release branch are here<https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>)
Feel free to restore our default records and broaden their parameters to match all your scan types.
re Defaced, native, selected -- these filter the scans displayed as you move to the next page (View Session), instead of viewing "all types" of scans from a given session :
* "defaced" means that a defacing script<https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md> has masked the subject's face in the volume (for patient privacy)
* "native" means that no pre-processing has been performed on the scan (it's raw data),
* "selected" will show only volumes that have been QC'd and "selected" as the best of their type -- used to display only the best quality T1 image instead of all T1s acquired in a session, e.g.
re QC Comments --
Once you have successfully loaded scans (matched to the mri_protocol table), you'll be able to use the Imaging Browser's View Session subpage to enter/view QC comments on each volume, or for each visit.
These are stored directly in the database, and linked to each scan. (Table name: feedback_mri_comments)
(Visit-level QC comments are linked to the session.)
For a walkthrough of the Imaging setup - please see the Imaging Setup guide<https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md> -
An old LORIS walkthrough video<https://www.youtube.com/watch?v=HDWC6RUbI6A> can also walk you through some of the Imaging front-end features, starting at 8:00
LORIS' imaging modules have been updated many times since this video, but the functionality and workflow is similar.
Let us know how it goes once you have entries in your mri_protocol table -
Best,
Christine
On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi Christine,
In the candidate_list page i can see this patient
[image.png]
If i press the link under PSCID i get to see
[image.png]
and if i press the link under Scan Done it redirects me to imaging_browser
[image.png]
At the mri_violations page i also see No results ( neither on resolved / not resolved ).
At the imaging_uploader i can see the record that failed.
[image.png]
If i click on the tarchive info i get to see the Protocol Name which i think is the acquisition we wanted?
[image.png]
Also my mri_protocol table is empty.
Furthermore i would like to ask about the defaced, native, selected. What exactly is native and selected? And where are the qc comments stored?
[image.png]
Finally a walkthrough would be helpful.
Thanks,
Sotirios
Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,
Glad to hear you're making progress with the visit labels. To follow up on your last few emails:
a- The Wiki's Setup Guide contains Sample insert statements for the Visit Windows table<https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>.
As Cecile mentioned, the consistency of visit label format is important: V01, v01, V1, 01 -- whichever you select to use is fine; we use V01 by default across all documentation.
b- For Password reset, there is a script in the tools/ directory so that a back-end administrator can reset any front-end user password, including Admin. (See info on setting up / resetting User passwords in the Wiki's Setup Guide<https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>)
c- The minc file not being registered -- due to AcquisitionProtocol unknown.
This means the SeriesDescription (Acquisition Protocol) in you Dicom header was not matched to any scan listed in the mri_protocol database table.
(In the online Loris-MRI Troubleshooting Guide,<https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this is Table 3, 2nd-last item "no MINCs inserted").
The MRI Violations module (Readme here) <https://github.com/aces/Loris/tree/minor/modules/mri_violations> will show you the details of this mismatch --
Go to the module (under the Imaging menu), find your scan and click the link "Could not identify scan type" -- in the next subpage you can compare the scan's actual parameters against the mri_protocol table.
To resolve this, adjust your mri_protocol table values or perhaps ensure your DICOMs are labelled consistently.
Let us know if this works for you -- we can also walk you through an example of non-identified scans on Demo.loris.ca<http://Demo.loris.ca> (MRI Violations module).
Best,
Christine
The LORIS team
On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
I hope this is sufficient as the error for the visit label disappeared.
[image.png]
Please see the attached file. Also something i found.
lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-17-39-xubBdv.log
==> Loading file from disk /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
--> mapping DICOM parameter for /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
==> computing md5 hash for MINC body.
--> md5: 6b1202fd63e29de4c9be1cd9925888a5
==> verifying acquisition protocol
Acquisition protocol is unknown
--> The minc file cannot be registered since the AcquisitionProtocol is unknown
Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Ok I fixed the login problem by using a known hash and by deleting the rows from the login_history i was able to login.
Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Hi,
there was no visit label 01 in the Visit_Windows table and i don't know how to insert it because the record requires lots of attributes. Also the system for a reason asked me to update my password and now i don't remember it and my account got suspended. Is there a way to reset it or set a simple password? I updated the password hash in the users table by using the hash from another LORIS setup we had and i still couldn't login ( also the attribute password is always NULL and the expiration date is 1999-01-01 for some reason ).
Thanks
Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
Can you try adding the visit label v01 to the Visit_Windows table?
However, I noticed that in a previous dataset, the label was V1. Does that refer to the same visit? If so, you might want to harmonize the visit labels so they are all the same across datasets for a given timepoint, meaning you will need to relabel scans when the visit label is different but referring to the same visit label (v01 = V1 etc...).
Hope this helps,
Cécile
On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi,
Could you help me with the "Visit label does not exist"? I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but it appears that this problem hasn't been resolved yet.
lorisadmin at hbp:/data/loris/bin/mri$ cat /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
==> Loading file from disk /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
--> mapping DICOM parameter for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
--> using user-defined filterParameters for /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
Candidate Mismatch Error is Visit label does not exist
-> WARNING: This candidate was invalid. Logging to
MRICandidateErrors table with reason Visit label does not exist
Thank you,
Sotirios
Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Hi Cecile,
The Center error was fixed. Still the insertion of mincs fails. Please see the output.txt file i attached. Also is there something else i need to change at the paths configuration?
Thank you,
Sotirios
Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
We are making progress!
I have a feeling this error comes from the fact that your psc table does not have the MRI_alias populated for the DCC site. Running the following query in the mysql database should fix this:
UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE Name="Data Coordinating Center";
Repeat the same with all your sites (make sure to change the Aliases between sites, they should all be unique).
Let me know how it goes!
Best,
Cécile
On Thu, Jul 25, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Dear Cecile,
You were right about your guesses. I did the modifications you suggested, i still get the "no mincs inserted" error, now i am getting the "No center found this candidate" error ( how do i fix that? from what i see the .dcm files contains a 'Institution Name', is that the center? ), so i guess that's why the validation fails, but i changed the force variable of tarchiveLoader to 1, shouldn't it have inserted the mincs then? Also it is optional to have a mail server, right? ( from what i see the mail error does not affect the $valid_study, so i assume we are okay with that )
Thank you a lot,
Sotirios
Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
From what I understand, I believe you just need to update a few config settings from the frontend in the Config module (under the Admin menu).
[Screen Shot 2019-07-25 at 10.31.35 AM.png]
Then go to the Paths section of the config module and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess is that currently, it is set to /data/LORIS/data) and click on the submit button.
[Screen Shot 2019-07-25 at 10.32.50 AM.png]
Then, go to Imaging Pipeline section of the Configuration module and update the "Loris-MRI Data Directory" to /data/loris/data/ (my guess is that it is empty at the moment in your database which is why $data_dir is not defined when you run the tarchiveLoader step of the insertion pipeline).
[Screen Shot 2019-07-25 at 10.40.52 AM.png]
Finally, I took a look at your environment file and it might be a good idea to update your PERL5LIB variable to the following (it has been added to the code a few releases ago as we realized this was needed for the libraries. Not sure which version of LORIS-MRI you are using but it does not hurt to update this variable to what I suggest below):
export PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
Hope this helps. Sorry you are experiencing so much trouble setting things up. We probably need to update our WIKI.
Best,
Cécile
On Thu, Jul 25, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
The "Loris-MRI Data Directory" should be in the environment file?
Στις Πέμ, 25 Ιουλ 2019 στις 12:59 π.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
The scripts are located in /data/loris/bin/mri/. Somewhere I might have messed something up but i remember following the instructions in the wiki.For example when i tried to execute the batch_uploads_imageuploader perl script the line
my $command = "$bin_dir/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> "
was pointing to an invalid path, for example: it was repeating a pattern and had LORIS instead of loris ( i think the mistake was that in the wiki it suggested to use $PROJECT for the name of the folder and i choosed 'loris' https://github.com/aces/Loris/wiki/Imaging-Database ). See also the in image for the modification i did. Also i didn't find the section to config the $data_dir variable.
Thank you,
Sotirios
Στις Τετ, 24 Ιουλ 2019 στις 6:05 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
It looks like you have one Config setting not set (based on the first error message you got when running it the first time). You need to set a value for "Loris-MRI Data Directory" in the Config module under the Imaging pipeline section (from what I can see, it would be /data/loris/data/ for your setup).
The reason you got that error message the second time is that the pipeline checks if the DICOM study was already inserted in the tarchive table. Since you ran the study once already, the study is inserted into the tarchive, hence the message. However, the pipeline did not complete as the MINC files were not created and inserted into the files/parameter_file table. In order to continue the insertion, you will then need to run the tarchiveLoader command suggested in the terminal during the second run:
/data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose
Finally, I am a bit confused by your setup. Where are the scripts located? In /data/loris/bin/mri or /data/loris/data? It feels like the Config setting "LORIS-MRI code" in the Paths section was set to "/data/LORIS/data" but it should have been set to the directory where the scripts are located (most probably /data/loris/bin/mri).
Hope this helps,
Cécile
On Wed, Jul 24, 2019 at 10:55 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Ok first i execute this command:
"lorisadmin at hbp:/data/loris/bin/mri$ ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143.
Use of uninitialized value $data_dir in concatenation (.) or string at ./batch_uploads_imageuploader line 143.
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader line 147.
base is DCC0000_258024_V01
path is /data/incoming/
type is .tar.gz
fullpath is /data/incoming/DCC0000_258024_V01.tar.gz
source /tmp/ImagingUpload-17-43-ZUEFjb
targetlocation /data/loris/data/tarchive
Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/tarchive_validation.pl<http://tarchive_validation.pl> line 219.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl<http://minc_insertion.pl> line 270.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
Can't exec "mail": No such file or directory at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
print() on closed filehandle MAIL at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
Use of uninitialized value $data_dir in concatenation (.) or string at /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
No Mincs inserted
The tarchiveLoader insertion script has failed.
Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
I inserted the VisitLabel, but still the Mincs are not inserted and i am getting this error
"lorisadmin at hbp:/data/loris/bin/mri$ /data/loris/data/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -upload_id 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd -name '__MACOSX' -delete
Spool message is:
The Scan for the uploadID 3 has already been run with tarchiveID: 7.
To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar -verbose"
Which files should i delete? I thought that deleting the files from the tarchive was enough. And i executed the last proposed command to continue to rest of the insertion pipeline ( check the image ).
Thank you
Στις Τετ, 24 Ιουλ 2019 στις 5:05 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
Sorry I was not clear before. Every visits of candidates are created in the session table with one entry per CandID/VisitLabel. So if the imaging pipeline created visits in the session table (that are not attached to instruments) and you want to clean your database completely, you can delete entries in that table as well.
Regarding your point 2, the imaging pipeline can create the visit in the session table as long as the visit label is present in the Visit_Windows table (which means the visit label stored in the PatientName is a valid visit label).
However, in your prod file, if the variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the visit label should be created in the Visit_Windows table I believe. Here is the line of the prod file you would need to change<https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>.
In general, we prefer populating the Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for candidate data to avoid insertion of badly labelled MRI data that are complex to relabel.
Finally, regarding the candidate creation, if you execute the following steps, the pipeline should be able to create candidates:
- set in the Imaging Pipeline section of the config module the config setting "Upload creation of candidates" to Yes
- manually transfer the scans to the LORIS server instead of uploading it via the imaging browser
- run batch_imaging_upload.pl<http://batch_imaging_upload.pl> as you did until now.
Hope this helps!
Best,
Cécile
On Wed, Jul 24, 2019 at 8:47 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
About my second question i replaced the name of the patient in the .dcm files and now i am getting an error that the visit label does not exist.
I thought it was supposed to be automatically created.
"Done adding archive info into database
/data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar -verbose
md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
candidate id 258024
=> No Visit labelVisit label does not exist
Set centerID = 1
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
Number of MINC files that will be considered for inserting into the database: 1
log dir is /logs and log file is /logs/TarLoad-15-42-L6pocU.log
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
PSCID is: DCC0000
CandID id: 258024
visit_label is: V1
candidate id 258024
=> No Visit label
Cleaning up temp files: rm -rf /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
Στις Τετ, 24 Ιουλ 2019 στις 3:38 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Hi,
1) What are the records in the session table?
2) I tried to upload a non-phantom file like this
input_file.txt:
/data/incoming/DCC0000_258024_V1.tar.gz N DCC0000_258024_V1
Terminal:
./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
and i get the following error in the log.txt file
"Running now the following command: /data/loris/data/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
find -path \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
Spool message is:
The PatientName read from the DICOM header does not start with DCC0000_258024_V1 from the mri_upload table
"
and the spool message is repeated for each .dcm file. Should i preprocess every .dcm file and change the PatientName to "DCC0000_258024_V1"?
3) As far as it concerns the candidate profile i have to create a new one each time before i try to upload a file? Is there already a way to create a candidate profile and get the DCCID and PSCID without the user interface?
Thank you,
Sotirios
Στις Πέμ, 18 Ιουλ 2019 στις 5:00 μ.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Hi Sotirios,
See answers to your questions below.
About the 1st case we had a dicom with a blank studyUID, maybe someone accidentally removed it.
That is strange. Something must have been done to the DICOM files. I have never seen a study with no StudyUID out of the scanner. Usually, you need to manually erase it with some tool. However, DICOMs never cease to surprise me...
Some other questions:
1) What are the steps to remove all of my patients and uploads?: because i want to try to reupload all the testing dicoms we had with a clean database.
Release 21.0 of LORIS-MRI will offer a script to remove all the entries and files specific to an upload. However, this release is not yet out. Hopefully in the next few weeks.
In the meantime, since your case is particular and that you just want to start with a clean database, the following deletes should work (hopefully I won't forget any tables):
delete from mri_violations_log;
delete from mri_protocol_violated_scans;
delete from MRICandidateErrors;
delete from parameter_file;
delete from files_qcstatus; # (if you played with the QC part of the imaging browser for testing)
delete from feedback_mri_comments; # (if you played with the QC part of the imaging browser for testing)
delete from tarchive_series;
delete from tarchive_files;
delete from mri_upload;
delete from tarchive;
delete from mri_scanner;
delete from candidate where PSCID="scanner";
I don't know if you want to also delete entries in the session and candidate table too?
2) We do not need to create the profile of a patient ( are the patients stored in the candidate table? because i can't see the ghosts ), because will it automatically be created when importing a dicom?
I am not sure I understand fully this question. All candidates are stored in the candidate table. The phantom scans however are attached to a scanner candidate depending on where the scan happened. It is a bit of a weird concept that we have to redesign eventually but never got a chance to get to it.
Hopefully this answered your question, otherwise, don't hesitate to let me know.
3) What is the difference between uploading a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel?
When you upload the scan as PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs and visit label are valid at the time of upload.
When you upload a scan as phantom, it expects that the DICOM field PatientName and uploaded filename contains the string "phantom". We enforced this behaviour on the imaging uploader side in recent releases but I can't remember which one. Probably the upcoming 21.0 release.
All those verifications might seem cumbersome but they are here to ensure that the files inserted are all valid and labelled properly as it is a bit messy to have to delete files that were wrongly labelled. At least, the delete script present in release 21.0 will make this process easier but it is still good practice to verify those things.
Thank you,
With pleasure. Hopefully the answers to your questions will be helpful.
Best,
Cécile
PS: loris-dev mailing list: you will find the initial answer I gave Sotirios below. I forgot to cc the loris-dev in my earlier reply...
Στις Τρί, 16 Ιουλ 2019 στις 12:02 π.μ., ο/η Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> έγραψε:
Dear Sotirios,
Thank you for reaching out. Since your email was already organized in points, I will reply directly below your questions below.
Best,
Cécile
1) What do we do when the StudyUID is blank on the header? https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md There solution provided at the table 3 does not guide us how to find the information ( is possible ).
The StudyUID is the field used in our pipeline at the moment to check whether a DICOM study was already inserted into LORIS with that same StudyUID since it is supposed to be unique for every single study. Currently, we do not support insertion of DICOM studies if they do not have a StudyUID associated with them.
Is there a specific reason why the StudyUID is blank in the DICOM headers in your DICOM files? Did they go through some processes before upload to LORIS?
2) When i am about to upload a non-phanton case i need a 'Visit Label'. Is there already a script that can create a new visit label for a specific Candidate, so i can provide it as input afterwards to the
batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
I am not sure if the front-end allows for it but if you use batch_uploads_imageuploader, the insertion scripts could create the visit label for you. However, it does need to be included in the patient name in order for the script to know which label it should use.
For example: you upload V02 for MTL0123 (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion scripts will create a V02 visit for MTL0123 if the PatientName field for the dataset is MTL0123_456789_V02 with Stage marked as "Not Started".
However, note that for the script to create the visit for the candidate, you have to make sure that all the visit label of your projects were inserted in the Visit_Windows table (otherwise, the visit will never be created as they were not specified as being part of the list of visit label to expect). So in the example above, you should have one row in Visit_Windows with Visit_label="V02" set.
3) Section 4.3 https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
What do we do when the folder contains multiple mnc files?
This is a case by case. Most of the time, the MINC files that failed insertion into the imaging browser end up in the MRI violation module where you can see what went wrong with the acquisitions not inserted. If you notice that the MINC file should be inserted as a specific protocol, you can force the insertion as explained in section 4.3.
In your case, I have a feeling that you want to be able to insert MINC files that did not go through the whole pipeline insertion (DICOM archival, then dcm2mnc, then protocol identification, then insertion...). In theory, you could call minc_insertion.pl<http://minc_insertion.pl> on any MINC file, provided you have at least the following information:
- path to the MINC file
- uploadID associated with the MINC files or DICOM archive path from which those MINC files were created from
Then the minc_insertion.pl<http://minc_insertion.pl> script will do the subject information and protocol validation etc...
If all the MINC files come from the same uploadID or TarchiveID, then you could run a loop in bash calling the minc_insertion.pl<http://minc_insertion.pl> script like this for files deriving from uploadID=1:
ls /path/to/mnc/folder/* | while read f; do minc_insertion.pl<http://minc_insertion.pl> -profile prod -uploadID 1 -mincPath $f; done
Thank you,
Hope this helped!
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McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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Montreal Neurological Institute
McGill University | Montreal | Canada
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Montreal Neurological Institute
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