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Add phase encoding direction and echo number to mri protocol and mri protocol violated scans #782

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Merged
merged 12 commits into from
Aug 18, 2022
Merged

Add phase encoding direction and echo number to mri protocol and mri protocol violated scans #782

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e2075cd
add PhaseEncodingDirection and ScanOptions to mri_protocol and mri_pr…
cmadjar Aug 10, 2022
6c2ba4f
update perl code to add the new fields in mri_protocol and mri_protoc…
cmadjar Aug 10, 2022
b600cc0
fix ScanOptions not being inserted correctly
cmadjar Aug 10, 2022
ab43738
use EchoNumber instead of ScanOptions as more generic
cmadjar Aug 10, 2022
458da2c
update doc
cmadjar Aug 10, 2022
943b788
fix seriesUID not being inserted in mri_protocol_violated_scans
cmadjar Aug 11, 2022
5c69ae9
some print to figure out why scan is not inserted?
cmadjar Aug 11, 2022
ba4ea5c
some print to figure out why scan is not inserted?
cmadjar Aug 11, 2022
1898d6f
fix tiny bug
cmadjar Aug 11, 2022
162060b
other prints
cmadjar Aug 11, 2022
5c70b16
other prints
cmadjar Aug 11, 2022
f019129
fix comparison of int and str for echo number comparison between prot…
cmadjar Aug 11, 2022
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4 changes: 3 additions & 1 deletion docs/scripts_md/MRI.md
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ INPUTS:

RETURNS: textual name of scan type from the `mri_scan_type` table

### insert\_violated\_scans($dbhr, $series\_desc, $minc\_location, $patient\_name, $candid, $pscid, $visit, $tr, $te, $ti, $slice\_thickness, $xstep, $ystep, $zstep, $xspace, $yspace, $zspace, $time, $seriesUID, $data\_dir)
### insert\_violated\_scans($dbhr, $series\_desc, $minc\_location, $patient\_name, $candid, $pscid, $visit, $tr, $te, $ti, $slice\_thickness, $xstep, $ystep, $zstep, $xspace, $yspace, $zspace, $time, $seriesUID, $echo\_numbers, $phase\_enc\_dir, $data\_dir, $mriProtocolGroupID)

Inserts scans that do not correspond to any of the defined protocol from the
`mri_protocol` table into the `mri_protocol_violated_scans` table of the
Expand Down Expand Up @@ -116,6 +116,8 @@ INPUTS:
- $tarchiveID : `TarchiveID` of the DICOM archive from which this file is derived
- $image\_type : the `image_type` header value of the image
- $data\_dir : path to the LORIS MRI data directory
- $echo\_numbers : `echo_numbers` of the image (a.k.a. `dicom_0x0018:el_0x0086` header)
- $phase\_enc\_dir : `phase_encoding_direction` of the image
- $mriProtocolGroupID : ID of the protocol group used to try to identify the scan.

### scan\_type\_id\_to\_text($typeID, $db)
Expand Down
10 changes: 9 additions & 1 deletion python/lib/imaging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,6 +199,8 @@ def insert_protocol_violated_scan(self, patient_name, cand_id, psc_id, tarchive_
:type mri_protocol_group_id: int
"""

phase_encoding_dir = scan_param["PhaseEncodingDirection"] if "PhaseEncodingDirection" in scan_param else None

info_to_insert_dict = {
"CandID": cand_id,
"PSCID": psc_id,
Expand All @@ -218,8 +220,10 @@ def insert_protocol_violated_scan(self, patient_name, cand_id, psc_id, tarchive_
"ystep_range": scan_param["ystep"] if "ystep" in scan_param.keys() else None,
"zstep_range": scan_param["zstep"] if "zstep" in scan_param.keys() else None,
"time_range": scan_param["time"] if "time" in scan_param.keys() else None,
"SeriesUID": scan_param["SeriesUID"] if "SeriesUID" in scan_param.keys() else None,
"SeriesUID": scan_param["SeriesInstanceUID"] if "SeriesInstanceUID" in scan_param.keys() else None,
"image_type": str(scan_param["ImageType"]) if "ImageType" in scan_param.keys() else None,
"PhaseEncodingDirection": phase_encoding_dir,
"EchoNumber": repr(scan_param["EchoNumber"]) if "EchoNumber" in scan_param else None,
"MriProtocolGroupID": mri_protocol_group_id if mri_protocol_group_id else None
}
self.mri_prot_viol_scan_db_obj.insert_protocol_violated_scans(info_to_insert_dict)
Expand Down Expand Up @@ -636,6 +640,8 @@ def is_scan_protocol_matching_db_protocol(self, db_prot, scan_param):
scan_ti = scan_param['InversionTime'] * 1000 if 'InversionTime' in scan_param else None
scan_slice_thick = scan_param['SliceThickness']
scan_img_type = str(scan_param['ImageType'])
scan_ped = scan_param['PhaseEncodingDirection'] if 'PhaseEncodingDirection' in scan_param else None
scan_en = scan_param['EchoNumber'] if 'EchoNumber' in scan_param else None

if (self.in_range(scan_param['time'], db_prot['time_min'], db_prot['time_max'])) \
and self.in_range(scan_tr, db_prot['TR_min'], db_prot['TR_max']) \
Expand All @@ -648,6 +654,8 @@ def is_scan_protocol_matching_db_protocol(self, db_prot, scan_param):
and self.in_range(scan_param['yspace'], db_prot['yspace_min'], db_prot['yspace_max']) \
and self.in_range(scan_param['zspace'], db_prot['zspace_min'], db_prot['zspace_max']) \
and self.in_range(scan_slice_thick, db_prot['slice_thickness_min'], db_prot['slice_thickness_max'])\
and (not db_prot['PhaseEncodingDirection'] or scan_ped == db_prot['PhaseEncodingDirection'])\
and (not db_prot['EchoNumber'] or scan_en == int(db_prot['EchoNumber']))\
and (not db_prot['image_type'] or scan_img_type == db_prot['image_type']):
return True

Expand Down
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