[Loris-dev] [LORIS-IPMSA] Series description does not match
Morales Pinzon, Alfredo
AMORALESPINZON at bwh.harvard.edu
Thu Dec 20 09:23:08 EST 2018
Hi Christine,
If I re-run the insertion pipeline will the "misclassify images" be correctly classified or I will have duplicates with different classification? I can easily re-run the pipeline but want to make sure I won't have duplicates.
Thank you very much for your answer.
Best,
Alfredo.
________________________________
From: Christine Rogers <rogers at bic.mni.mcgill.ca>
Sent: Wednesday, December 19, 2018 12:59:35 PM
To: Morales Pinzon, Alfredo
Cc: loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D.
Subject: Re: [Loris-dev] [LORIS-IPMSA] Series description does not match
External Email - Use Caution
Hi Alfredo,
Thanks for your feedback, we'll look to clarify those regex specs in our documentation for future releases.
Regarding changing the scan type -- the `files` table has an `AcquisitionProtocolID` column which references the mri_scan_type`table's `ID` column.
It's possible you may wish to re-run the insertion pipeline to identify and generate properly-labelled MINC filenames instead of undertaking manual updates in the filesystem and in the database.
Best,
Christine
On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,
I found the error, the column series_description_regex in table mri_protocol needs to be in a specific format, meaning that the initial "/" and ending "/i" must not be placed in the regex string. I replaced "series_description_regex: /^flr$/i" by "series_description_regex: flr *$" and now I have the correct classification when inserting a new image.
Now, I just need help with the images that were classified as NA (see my previous email), how can I change the type assigned to this images?
Additionally, I didn't find any documentation regarding the format of the regex that LORIS is expecting, I would be great if we can add it for future users. Also, does it make sense to have the last part of the regex hard coded as "/i"? Maybe a user would like to use "/x" or other options.
Thank you for your help.
Best regards,
Alfredo.
________________________________
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 Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Sent: Monday, December 17, 2018 9:27:28 PM
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>
Cc: Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com<mailto:pistikem at gmail.com>; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, Charles,M.D.
Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match
External Email - Use Caution
Dear LorisDev team,
I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS but they are not being classified correctly based on the series description (series_description_regex in table mri_protocol). Could you help with 2 things?
1. How can I change the type of an image already inserted? All the images inserted, so far around 240, were classified as NA.
2. Could you tell me if I am missing something in the series_description_regex in table mri_protocol? Here is what I have in the table mri_protocol and mri_scan_type, and a screenshot (attached) of one of the inserted images in LORIS:
-----------------------------------------------------------------------------
mysql> select * from mri_protocol \G;
*************************** 1. row ***************************
ID: 1004
Center_name: ZZZZ
ScannerID: 0
Scan_type: 41
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: /^flr$/i
*************************** 2. row ***************************
ID: 1005
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1001
TR_range: NULL
TE_range: NULL
TI_range: NULL
slice_thickness_range: NULL
FoV_x_range: NULL
FoV_y_range: NULL
FoV_z_range: NULL
xspace_range: NULL
yspace_range: NULL
zspace_range: NULL
xstep_range: NULL
ystep_range: NULL
zstep_range: NULL
time_range: NULL
series_description_regex: /^pdw$/i
*************************** 3. row ***************************
ID: 1007
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1002
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: /^t2w$/i
*************************** 4. row ***************************
ID: 1009
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1003
TR_range: NULL
TE_range: NULL
TI_range: NULL
slice_thickness_range: NULL
FoV_x_range: NULL
FoV_y_range: NULL
FoV_z_range: NULL
xspace_range: NULL
yspace_range: NULL
zspace_range: NULL
xstep_range: NULL
ystep_range: NULL
zstep_range: NULL
time_range: NULL
series_description_regex: /^t1c$/i
*************************** 5. row ***************************
ID: 1010
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1004
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: /^t1p$/i
*************************** 6. row ***************************
ID: 1011
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1005
TR_range: NULL
TE_range: NULL
TI_range: NULL
slice_thickness_range: NULL
FoV_x_range: NULL
FoV_y_range: NULL
FoV_z_range: NULL
xspace_range: NULL
yspace_range: NULL
zspace_range: NULL
xstep_range: NULL
ystep_range: NULL
zstep_range: NULL
time_range: NULL
series_description_regex: /^mtOFF$/i
*************************** 7. row ***************************
ID: 1012
Center_name: ZZZZ
ScannerID: 0
Scan_type: 1006
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: /^mtON$/i
*************************** 8. row ***************************
ID: 1013
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
8 rows in set (0.00 sec)
-----------------------------------------------------------------------------
mysql> select * from mri_scan_type;
+------+--------------+
| ID | Scan_type |
+------+--------------+
| 40 | fMRI |
| 41 | flair |
| 44 | t1 |
| 45 | t2 |
| 46 | pd |
| 47 | mrs |
| 48 | dti |
| 49 | t1relx |
| 50 | dct2e1 |
| 51 | dct2e2 |
| 52 | scout |
| 53 | tal_msk |
| 54 | cocosco_cls |
| 55 | clean_cls |
| 56 | em_cls |
| 57 | seg |
| 58 | white_matter |
| 59 | gray_matter |
| 60 | csf_matter |
| 61 | nlr_masked |
| 62 | pve |
| 999 | unknown |
| 1000 | NA |
| 1001 | pdw |
| 1002 | t2w |
| 1003 | t1c |
| 1004 | t1p |
| 1005 | mtOFF |
| 1006 | mtON |
+------+--------------+
-----------------------------------------------------------------------------
Thank you for any help.
Best regards,
Alfredo.
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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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