[Loris-dev] Error: Acquisition protocol is unknown
Morales Pinzon, Alfredo
AMORALESPINZON at bwh.harvard.edu
Tue Nov 28 16:20:01 EST 2017
Hi Mouna.
The error was coming from the 'NULL' entries in the "mri_protocol", I have modified them and the insertion is working.
Thank you very much!
Best,
Alfredo.
________________________________
From: Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca>
Sent: Tuesday, November 28, 2017 1:48:35 PM
To: Morales Pinzon, Alfredo; loris-dev at bic.mni.mcgill.ca
Cc: Louis Collins, Dr.; Sridar Narayanan, Dr.; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: Re: Error: Acquisition protocol is unknown
Hi Alfredo,
Which version of Loris-MRI are you on?
A couple of things that I can ask you to check:
1) instead of selecting from the mri_protocol at the mysql command, can you get a dump of the mri_protocol table into a text file. That row entry corresponding to ID=1008, does it have NULL or 'NULL' entries? i.e. when you inserted it, did you insert the NULL values with a single quotation? if so, this might be the issue
2) in your prod file, what is inside the routine: isFileToBeRegisteredGivenProtocol{}
3) in the mri_scan_types, I assume you have a scan_type entry for ID=1008?
4) the print statements you have enabled is a great start. I would add manually a few more a few lines later;
i.e. when the script does this:
else {
if ((!$rowref->{'TR_range'} || &in_range($tr, $rowref->{'TR_range'}))
&& (!$rowref->{'TE_range'} || &in_range($te, $rowref->{'TE_range'}))
...
}
I would add inside this if statement a few print. If the NULL comparison is working, the condition !$rowref->{'TR_range'} should be true, same thing for !$rowref->{'TE_range'}, etc..., so try to see if this is indeed the case by printing it.
Let me know if this helps, otherwise, do not hesitate to ask more!
- Mouna
________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu>
Sent: Tuesday, November 28, 2017 11:47:44 AM
To: loris-dev at bic.mni.mcgill.ca
Cc: Louis Collins, Dr.; Sridar Narayanan, Dr.; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; Zografos Caramanos, Mr; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: [Loris-dev] Error: Acquisition protocol is unknown
Dear LORIS team,
I am in the final phase of image batch-uploading using the script "batch_uploads_imageuploader" and need some help. It seems that everything goes well before the 'acquisition protocol" checking step, where the type of image cannot be determined and it's left as "unknown". It is strange that this happens because the parameters of the images are inside the ranges specified in the table "mri_protocol", and even stranger when I have an entry, for type NA, with everything NULL:
-------------------------------------------------------------------------------
mysql> select * from mri_protocol where ID=1008 \G;
*************************** 1. row ***************************
ID: 1008
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1000
TR_range: NULL
TE_range: NULL
TI_range: NULL
slice_thickness_range: NULL
FoV_x_range: NULL
FoV_y_range: NULL
FoV_z_range: NULL
xspace_range: NULL
yspace_range: NULL
zspace_range: NULL
xstep_range: NULL
ystep_range: NULL
zstep_range: NULL
time_range: NULL
series_description_regex: NULL
1 row in set (0.00 sec)
-------------------------------------------------------------------------------
I was trying to see where the error can comes from and it seems to come from the file "Loris-MRI/uploadNeuroDB/NeuroDB/MRI.pm" (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm). I actually activate the printing part of the code (https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L435 and https://github.com/aces/Loris-MRI/blob/950c9e8892773a7ecc9b97a117bdae74814ce8f1/uploadNeuroDB/NeuroDB/MRI.pm#L485) to see the parameter values of the images.
Here are the instruction that I am using and the logs that I get (I removed information related to my project by PPP):
Instruction
-------------------------------------------------------------------------------
PPP/bin/mri//batch_uploads_imageuploader -profile prod < PPP.txt > PPP_log_batch_uploads_imageuploader.txt 2>&
-------------------------------------------------------------------------------
File: log from batch_uploads_imageuploader script (PPP_log_batch_uploads_imageuploader.txt)
-------------------------------------------------------------------------------
Running now the following command: PPP/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 5 PPP.tar.gz -verbose
PPP/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-11-6-0NOcLo PPP/data/tarchive -clobber -database -profile prod -verbose
Source: /tmp/ImagingUpload-11-6-0NOcLo
Target: PPP/data/tarchive
Testing for database connectivity.
Database is available.
You will archive the dir : ImagingUpload-11-6-0NOcLo
You are creating a tar with the following command:
tar -cf PPP/data/tarchive/ImagingUpload-11-6-0NOcLo.tar ImagingUpload-11-6-0NOcLo
getting md5sums and gzipping!!
* Taken from dir : /tmp/ImagingUpload-11-6-0NOcLo
* Archive target location : PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar
* Name of creating host : PPP
* Name of host OS : PPP
* Created by user : lorisadmin
* Archived on : 2017-11-28 11:06:33
* dicomSummary version : 1
* dicomTar version : 1
* md5sum for DICOM tarball : 12c2e901dbb88a7cbcb71ede54ff2fdf ImagingUpload-11-6-0NOcLo.tar
* md5sum for DICOM tarball gzipped : 9fc33ff9fbd72a4c5aa14d4c6235c238 ImagingUpload-11-6-0NOcLo.tar.gz
* md5sum for complete archive : 5afa4143e07d50a2e340ddf45b5338d9 PPP_ImagingUpload-11-6-0NOcLo.tar
Adding archive info into database
Removing temporary files from target location
Done adding archive info into database
PPP/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod PPP/data/tarchive/PPP_ImagingUpload-11-6-0NOcLo.tar -verbose
md5sum PPP/data/tarchive/DPPP_ImagingUpload-11-6-0NOcLo.tar
PSCID is: PPP
CandID id: PPP
visit_label is: PPP
candidate id PPP
PSCID is: PPP
CandID id: PPP
visit_label is: PPP
Number of MINC files that will be considered for inserting into the database: 5
log dir is PPP/data/logs and log file is PPP/data/logs/TarLoad-11-6-MewKHm.log
PSCID is: PPP
CandID id: PPP
visit_label is: PPP
candidate id PPP
tr: 2500
te: 12.1
ti:
st: 3
time;
xspace: 256
yspace: 256
zspace: 60
xstep: -0.9765723348
ystep: -0.9765625
zstep: 3.
Checking flair (41) (Axial PD =~ NULL)
xspace yspace zspace ST
Checking pdw (1001) (Axial PD =~ NULL)
TR TE xspace yspace zspace ST
Checking t1 (44) (Axial PD =~ NULL)
xspace yspace zspace ST
Checking t2w (1002) (Axial PD =~ NULL)
xspace yspace zspace ST
Checking NA (1000) (Axial PD =~ NULL)
...
... // the other 4 images //
...
Cleaning up temp files: rm -rf /tmp/TarLoad-11-6-FYfBtg/ImagingUpload-11-6-0NOcLo*
No Mincs inserted
The insertion scripts have failed
-------------------------------------------------------------------------------
File: $project/data/logs/TarLoad-11-6-MewKHm.log
-------------------------------------------------------------------------------
==> Loading file from disk /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc
--> mapping DICOM parameter for /tmp/TarLoad-11-6-FYfBtg/PPP_3e1_mri.mnc
==> computing md5 hash for MINC body.
--> md5: 2278a2f9c6f586a16316d41390a0c045
==> verifying acquisition protocol
Acquisition protocol is unknown
--> The minc file cannot be registered since the AcquisitionProtocol is unknown
-------------------------------------------------------------------------------
I can provide more information if needed.
Any help is welcomed :)
Regards,
Alfredo.
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