[Loris-dev] Import mri - scripts
Christine Rogers, Ms.
christine.rogers at mcgill.ca
Thu Sep 19 12:57:19 EDT 2019
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<mailto: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.png]
Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault, Mrs <melanie.legault2 at mcgill.ca<mailto: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<mailto:sotirisnik at gmail.com>>
Sent: September 13, 2019 10:15
To: Melanie Legault, Mrs <melanie.legault2 at mcgill.ca<mailto:melanie.legault2 at mcgill.ca>>
Cc: Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>>; loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto: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<mailto: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<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>>
Sent: September 13, 2019 9:43
To: Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>>
Cc: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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? ).
[https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y]
Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto: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.png]
[image.png]
Thanks
Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto: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<mailto:sotirisnik at gmail.com>> wrote:
I see that i can edit the values but not how to insert new rows.
[image.png]
If i choose Inserted with flag then will the minc be inserted?
[image.png]
Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto: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<mailto: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<mailto:sotirisnik at gmail.com>> έγραψε:
Hi,
From Dicat's view seems that dcmodify worked in both cases
[image.png]
[image.png]
For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier.
[image.png]
Thanks
Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto: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<mailto:sotirisnik at gmail.com>> wrote:
Here is the psc table
[image.png]
I created 2 candidates profiles through the interface
[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<http://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<mailto: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<mailto: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<http://batch_uploads_imageuploader.pl> -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 144.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
SET @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips Medical Systems';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
ERROR: The validation has failed. Either re-run the validation again and fix the problem. Or re-run tarchiveLoader.pl using -force to force the execution.
The tarchiveLoader.pl insertion script has failed.
Can't exec "mail": No such file or directory at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 251.
And second execution:
(loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl<http://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<http://batch_uploads_imageuploader.pl> line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://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<mailto: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<mailto: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<mailto: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 $mridir/dicom-archive/.loris_mri/database_config.py
Best,
Christine
On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi Christine,
If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically?
Thanks
[https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs]
Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,
Glad to hear your LORIS core install is up and working and all the front-end pages are loading.
> lorisadmin at loris-VirtualBox:/var/www/loris$ 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<mailto:sotirisnik at gmail.com>> wrote:
As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?
[image.png]
Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto: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
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Montreal Neurological Institute
McGill University | Montreal | Canada
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Montreal Neurological Institute
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