CT and MR Imaging

Amador Lagunas; Po-Ju Chen; Luis Ruiz; Gaurang Shah; Scott Lempka; Priyanka Gupta; Tim Bruns

Aug 20, 2025

CT and MR Imaging

DOI

https://dx.doi.org/10.17504/protocols.io.yxmvm978bl3p/v1

Amador Lagunas^1,2,
Po-Ju Chen^1,2,
Luis Ruiz^1,2,
Gaurang Shah³,
Scott Lempka^1,4,
Priyanka Gupta⁵,
Tim Bruns^1,2

¹Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI;
²Biointerfaces Institute, University of Michigan, Ann Arbor, MI;
³Department of Radiology, University of Michigan, Ann Arbor, MI;
⁴Department of Anesthesiology, University of Michigan, Ann Arbor, MI;
⁵Department of Urology, University of Michigan, Ann Arbor, MI

SPARC
Tech. support email: [email protected]

Amador C Lagunas

University of Michigan - Ann Arbor

DOI: https://dx.doi.org/10.17504/protocols.io.yxmvm978bl3p/v1

Protocol Citation: Amador Lagunas, Po-Ju Chen, Luis Ruiz, Gaurang Shah, Scott Lempka, Priyanka Gupta, Tim Bruns 2025. CT and MR Imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.yxmvm978bl3p/v1

Manuscript citation:

Lagunas A, Chen PJ, Ruiz L, et al. Factors Affecting Anal Sphincter Recruitment During Intraoperative Pudendal Nerve Stimulation: An Observational Study. International Urogynecology Journal. Published online 2025. doi:10.1007/s00192-025-06238-3

License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Protocol status: Working

We use this protocol and it's working

Created: November 06, 2024

Last Modified: August 20, 2025

Protocol Integer ID: 111712

Keywords: Imaging, implanted pudendal stimulation lead, pudendal stimulation lead, lead relative to the pudendal nerve, pudendal nerve stimulation, lead imaging, effects of pudendal nerve stimulation, pudendal nerve, ct scan, mr imaging, mri scan, mr imaging this protocol, implanted lead, scan, nerve, ct

Funders Acknowledgements:

National Institutes of Health SPARC

Grant ID: OT2OD028191

Abstract

This protocol summarizes the MRI scans used to visualize and segment the pudendal nerve i and the CT scan used to identify the location of an implanted pudendal stimulation lead. Together these scans can be used to determine the position of the implanted lead relative to the pudendal nerve. The nerve and lead imaging is a part of a larger study mapping the effects of pudendal nerve stimulation described in a separate protocol: dx.doi.org/10.17504/protocols.io.14egn3jezl5d/v1

Materials

3T MRI - Ingenia 3T system, Philips
CT Scanner - DiscoverCT750 HD or Revolution scanner, GE Healthcare

Troubleshooting

MR Imaging

3D_T1_PRE_FMRI_CS
An anatomic 3D T1 weighted axial sequence of lower abdomen and pelvis 
that can be reformatted in different orthogonal planes and allows us to 
trace the nerve roots and branches that make up pudendal nerve. 

Parameters:
EX_single_scan_id =		16825236;
SmartSelect =			"yes";
Coil 1  (exclude) =		"None";
Uniformity =			"CLEAR";
FOV          AP (mm) =		360;
             RL (mm) =		360;
             FH (mm) =		250;
ACQ voxel size   AP (mm) =	1;
             RL (mm) =		1;
             FH (mm) =		1;
Recon voxel size AP (mm) =	0.75;
             RL (mm) =		0.75;
             FH (mm) =		0.5;
Fold-over suppression =		"oversampling";
    L (mm) =			40;
    R (mm) =			40;
Slice oversampling =		"user defined";
    oversample factor =		1.29999995;
Reconstruction matrix =		480;
SENSE =				"no";
CS-SENSE =			"yes";
    reduction =			2.5;
    denoising =			"system default";
k-t Acceleration =		"no";
Stacks =			1;
    slices =			500;
    slice orientation =		"transverse";
    fold-over direction =	"RL";
    fat shift direction =	"P";
Multi-chunk =			"no";
O-MAR =				"no";
Large table movement =		"no";
PlanAlign =			"no";
REST slabs =			0;
Interactive positioning =	"no";
External control =		"no";
Patient position =		"head first";
Patient body position =		"head first";
Patient orientation =		"supine";
Patient body orientation =	"supine";
Scan type =			"Imaging";
Scan mode =			"3D";
    technique =			"SE";
Modified SE =			"no";
Acquisition mode =		"cartesian";
Fast Imaging mode =		"TSE";
    3D VIEW =			"no";
    shot mode =			"multishot";
TSE factor =			110;
    startup echoes =		4;
    profile order =		"linear";
    turbo direction =		"Z";
    DRIVE =			"yes";
    ultrashort =		"ultra";
    fid reduction =		"strong";
    3D non-selective =		"yes";
Echoes =			1;
    partial echo =		"no";
TE =				"shortest";
Flip angle (deg) =		90;
Refocusing control =		"PSS Adv (T2-opt)";
    min. angle  (deg) =		70;
    mid. angle (deg) =		90;
    max. angle (deg) =		120;
TR =				"user defined";
    (ms) =			2800;
Halfscan =			"yes";
    factor Y =			0.600000024;
    factor Z =			0.800000012;
Water-fat shift =		"maximum";
RF Shims =			"fixed";
Shim =				"default";
mDIXON =			"no";
Fat suppression =		"no";
Grad Rev Fat suppr =		"no";
Water suppression =		"no";
BB pulse =			"no";
MTC =				"no";
APT =				"no";
Custom prepulse =		"no";
MDME =				"no";
Diffusion mode =		"no";
T1 mapping =			"no";
Transmit channels =		"both";
SAR mode =			"high";
B1 mode =			"default";
SAR allow first level =		"no";
PNS mode =			"moderate";
Gradient mode =			"maximum";
SofTone mode =			"no";
Cardiac synchronization =	"no";
Heart rate > 250 bpm =		"no";
Respiratory compensation =	"no";
Navigator respiratory comp =	"no";
Flow compensation =		"no";
Motion smoothing =		"no";
NSA =				1;
MRE enable =			"no";
CENTRA =			"no";
Manual start =			"no";
Dynamic study =			"no";
Arterial Spin labeling =	"no";
Preparation phases =		"auto";
Interactive F0 =		"no";
Quick Survey =			"default";
B0 field map =			"no";
B1 field map =			"no";
MIP/MPR =			"no";
Images =			"M", (3) "no";
Autoview image =		"M";
Calculated images =		(4) "no";
Reference tissue =		"Male Pelvis";
Recon compression =		"No";
Preset window contrast =	"no";
Reconstruction mode =		"immediate";
Save raw data =			"no";
Hardcopy protocol =		"no";
Image filter =			"system default";
Uniformity correction =		"no";
Geometry correction =		"none";
Elliptical k-space shutter =	"default";
Stack Offc. AP (P=+mm) =	10.0683002;
            RL (L=+mm) =	-0.0122832758;
            FH (H=+mm) =	-32.6540947;
      Ang.  AP (deg) =		0;
            RL (deg) =		-0;
            FH (deg) =		-0;
      Free rotatable =		"no";
IF_info_seperator =		1634755923;
Extended Function. Opt. =	"6";
Total scan duration =		"11:12.0";
Rel. SNR =			1.87513769;
Act. TR (ms) =			"2800";
Act. TE (ms) =			"178";
ACQ matrix M x P =		"360 x 360";
ACQ voxel MPS (mm) =		"1.00 / 1.00 / 1.00";
REC voxel MPS (mm) =		"0.75 / 0.75 / 0.50";
Scan percentage (%) =		100;
Act. slice gap (mm) =		-0.5;
WFS (pix) / BW (Hz) =		"0.582 / 746.7";
TSE es / shot (ms) =		"3.7 / 435";
TEeff / TEequiv (ms) =		"178 / 117 ";
Min. TR (ms) =			"1734";
Local torso SAR =		"<  39 %";
Whole body SAR / level =	"< 1.2 W/kg / normal";
SED =				"< 0.8 kJ/kg";
Coil Power =			"37 %";
Max B1+rms =			"1.42 uT";
PNS / level =			"80 % / normal";
dB/dt =				"102.5 T/s";
Sound Pressure Level (dB) =	28.1958218;

OPT_CS_Ax_T2_3D_1mm
An anatomic 3D T2 weighted axial sequence of lower abdomen and pelvis 
that can be reformatted in different orthogonal planes. The goal is of 
making nerves stand out from the surrounding tissue.

Parameters:
EX_single_scan_id =		20666869;
SmartSelect =			"yes";
Coil 1  (exclude) =		"None";
Uniformity =			"CLEAR";
FOV          AP (mm) =		220;
             RL (mm) =		220;
             FH (mm) =		200;
ACQ voxel size   AP (mm) =	0.649999976;
             RL (mm) =		0.65180105;
             FH (mm) =		1;
Recon voxel size AP (mm) =	0.491071433;
             RL (mm) =		0.491071433;
             FH (mm) =		1;
Fold-over suppression =		"oversampling";
    L (mm) =			80;
    R (mm) =			80;
Slice oversampling =		"user defined";
    oversample factor =		2;
Reconstruction matrix =		448;
SENSE =				"no";
CS-SENSE =			"yes";
    reduction =			6;
    denoising =			"system default";
k-t Acceleration =		"no";
Stacks =			1;
    slices =			200;
    slice orientation =		"transverse";
    fold-over direction =	"RL";
    fat shift direction =	"P";
Multi-chunk =			"no";
O-MAR =				"no";
Large table movement =		"no";
PlanAlign =			"no";
REST slabs =			0;
Interactive positioning =	"no";
External control =		"no";
Patient position =		"head first";
Patient body position =		"head first";
Patient orientation =		"supine";
Patient body orientation =	"supine";
Scan type =			"Imaging";
Scan mode =			"3D";
    technique =			"SE";
Modified SE =			"no";
Acquisition mode =		"cartesian";
Fast Imaging mode =		"TSE";
    3D VIEW =			"no";
    shot mode =			"multishot";
TSE factor =			60;
    startup echoes =		4;
    profile order =		"linear";
    turbo direction =		"Y";
    DRIVE =			"yes";
    ultrashort =		"no";
    fid reduction =		"strong";
    3D non-selective =		"yes";
Echoes =			1;
    partial echo =		"no";
TE =				"shortest";
Flip angle (deg) =		90;
Refocusing control =		"constant";
    angle (deg) =		45;
    bright fat reduction =	"no";
TR =				"user defined";
    (ms) =			1800;
Halfscan =			"no";
Water-fat shift =		"maximum";
RF Shims =			"fixed";
Shim =				"default";
mDIXON =			"no";
Fat suppression =		"no";
Grad Rev Fat suppr =		"no";
Water suppression =		"no";
BB pulse =			"no";
MTC =				"no";
APT =				"no";
Custom prepulse =		"no";
MDME =				"no";
Diffusion mode =		"no";
T1 mapping =			"no";
Transmit channels =		"both";
SAR mode =			"high";
B1 mode =			"default";
SAR allow first level =		"no";
PNS mode =			"high";
Gradient mode =			"maximum";
SofTone mode =			"no";
Cardiac synchronization =	"no";
Heart rate > 250 bpm =		"no";
Respiratory compensation =	"no";
Navigator respiratory comp =	"no";
Flow compensation =		"no";
Motion smoothing =		"no";
NSA =				1;
MRE enable =			"no";
CENTRA =			"no";
Manual start =			"no";
Dynamic study =			"no";
Arterial Spin labeling =	"no";
Preparation phases =		"auto";
Interactive F0 =		"no";
Quick Survey =			"default";
B0 field map =			"no";
B1 field map =			"no";
MIP/MPR =			"no";
Images =			"M", (3) "no";
Autoview image =		"M";
Calculated images =		(4) "no";
Reference tissue =		"Grey matter";
Recon compression =		"No";
Preset window contrast =	"soft";
Reconstruction mode =		"real time";
Save raw data =			"yes";
Hardcopy protocol =		"no";
Image filter =			"system default";
Uniformity correction =		"no";
Geometry correction =		"default";
Elliptical k-space shutter =	"default";
Stack Offc. AP (P=+mm) =	10.0683002;
            RL (L=+mm) =	-0.0122832758;
            FH (H=+mm) =	-11.8124113;
      Ang.  AP (deg) =		0;
            RL (deg) =		-0;
            FH (deg) =		-0;
      Free rotatable =		"no";
IF_info_seperator =		1634755923;
Total scan duration =		"16:13.8";
Rel. SNR =			1.39131403;
Act. TR (ms) =			"1800";
Act. TE (ms) =			"291";
ACQ matrix M x P =		"340 x 337";
ACQ voxel MPS (mm) =		"0.65 / 0.65 / 1.00";
REC voxel MPS (mm) =		"0.49 / 0.49 / 1.00";
Scan percentage (%) =		99.1765747;
Act. slice gap (mm) =		0;
WFS (pix) / BW (Hz) =		"2.021 / 215.0";
TSE es / shot (ms) =		"8.4 / 548";
TEeff / TEequiv (ms) =		"291 / 132 ";
Min. TR (ms) =			"556";
Local torso SAR =		"<  8 %";
Whole body SAR / level =	"< 0.3 W/kg / normal";
SED =				"< 0.3 kJ/kg";
Coil Power =			"8 %";
Max B1+rms =			"0.66 uT";
PNS / level =			"76 % / normal";
dB/dt =				"104.6 T/s";
Sound Pressure Level (dB) =	23.9341621;

CS_COR_T2_3D 
An anatomic 3D T2 weighted sequence of lower abdomen and pelvis obtained
 in coronal plane, that can be reformatted in different orthogonal 
planes and allows us to trace the peripheral nerves, including nerve 
roots and branches that make up pudendal nerve. 

Parameters:
EX_single_scan_id =		63403658;
SmartSelect =			"yes";
Coil 1  (exclude) =		"None";
Uniformity =			"CLEAR";
FOV          FH (mm) =		220;
             RL (mm) =		220;
             AP (mm) =		148;
ACQ voxel size   FH (mm) =	0.649999976;
             RL (mm) =		0.651851833;
             AP (mm) =		2;
Recon voxel size FH (mm) =	0.491071433;
             RL (mm) =		0.491071433;
             AP (mm) =		2;
Fold-over suppression =		"oversampling";
    L (mm) =			110;
    R (mm) =			110;
Slice oversampling =		"user defined";
    oversample factor =		2;
Reconstruction matrix =		448;
SENSE =				"no";
CS-SENSE =			"yes";
    reduction =			6;
    denoising =			"system default";
k-t Acceleration =		"no";
Stacks =			1;
    slices =			74;
    slice orientation =		"coronal";
    fold-over direction =	"RL";
    fat shift direction =	"F";
Multi-chunk =			"no";
O-MAR =				"no";
Large table movement =		"no";
PlanAlign =			"no";
REST slabs =			0;
Interactive positioning =	"no";
External control =		"no";
Patient position =		"head first";
Patient body position =		"head first";
Patient orientation =		"supine";
Patient body orientation =	"supine";
Scan type =			"Imaging";
Scan mode =			"3D";
    technique =			"SE";
Modified SE =			"no";
Acquisition mode =		"cartesian";
Fast Imaging mode =		"TSE";
    3D VIEW =			"no";
    shot mode =			"multishot";
TSE factor =			60;
    startup echoes =		4;
    profile order =		"linear";
    turbo direction =		"Y";
    DRIVE =			"yes";
    ultrashort =		"no";
    fid reduction =		"strong";
    3D non-selective =		"yes";
Echoes =			1;
    partial echo =		"no";
TE =				"shortest";
Flip angle (deg) =		90;
Refocusing control =		"constant";
    angle (deg) =		45;
    bright fat reduction =	"no";
TR =				"user defined";
    (ms) =			1800;
Halfscan =			"no";
Water-fat shift =		"maximum";
RF Shims =			"fixed";
Shim =				"default";
mDIXON =			"no";
Fat suppression =		"no";
Grad Rev Fat suppr =		"no";
Water suppression =		"no";
BB pulse =			"no";
MTC =				"no";
APT =				"no";
Custom prepulse =		"no";
MDME =				"no";
Diffusion mode =		"no";
T1 mapping =			"no";
Transmit channels =		"both";
SAR mode =			"high";
B1 mode =			"default";
SAR allow first level =		"no";
PNS mode =			"high";
Gradient mode =			"maximum";
SofTone mode =			"no";
Cardiac synchronization =	"no";
Heart rate > 250 bpm =		"no";
Respiratory compensation =	"no";
Navigator respiratory comp =	"no";
Flow compensation =		"no";
Motion smoothing =		"no";
NSA =				1;
MRE enable =			"no";
CENTRA =			"no";
Manual start =			"no";
Dynamic study =			"no";
Arterial Spin labeling =	"no";
Preparation phases =		"auto";
Interactive F0 =		"no";
Quick Survey =			"default";
B0 field map =			"no";
B1 field map =			"no";
MIP/MPR =			"no";
Images =			"M", (3) "no";
Autoview image =		"M";
Calculated images =		(4) "no";
Reference tissue =		"Grey matter";
Recon compression =		"No";
Preset window contrast =	"soft";
Reconstruction mode =		"real time";
Save raw data =			"yes";
Hardcopy protocol =		"no";
Image filter =			"system default";
Uniformity correction =		"no";
Geometry correction =		"default";
Elliptical k-space shutter =	"default";
Stack Offc. AP (P=+mm) =	29.4671116;
            RL (L=+mm) =	-9.39104843;
            FH (H=+mm) =	-9.40761185;
      Ang.  AP (deg) =		0;
            RL (deg) =		-0;
            FH (deg) =		-0;
      Free rotatable =		"no";
IF_info_seperator =		1634755923;
Total scan duration =		"06:59.4";
Rel. SNR =			1.81962717;
Act. TR (ms) =			"1800";
Act. TE (ms) =			"291";
ACQ matrix M x P =		"340 x 337";
ACQ voxel MPS (mm) =		"0.65 / 0.65 / 2.00";
REC voxel MPS (mm) =		"0.49 / 0.49 / 2.00";
Scan percentage (%) =		99.1765747;
Act. slice gap (mm) =		0;
WFS (pix) / BW (Hz) =		"2.021 / 215.0";
TSE es / shot (ms) =		"8.4 / 548";
TEeff / TEequiv (ms) =		"291 / 132 ";
Min. TR (ms) =			"556";
Local torso SAR =		"<  8 %";
Whole body SAR / level =	"< 0.3 W/kg / normal";
SED =				"< 0.1 kJ/kg";
Coil Power =			"8 %";
Max B1+rms =			"0.66 uT";
PNS / level =			"60 % / normal";
dB/dt =				"98.9 T/s";
Sound Pressure Level (dB) =	20.8726139;

FAT_SAT_Ax_T2_3D_1mm
An anatomic 3D T2 weighted axial sequence of lower abdomen and pelvis 
that takes out bright fat signal and can be reformatted in different 
orthogonal planes. This allows the peripheral nerves to stand out and be
 better appreciated. 

Parameters:
EX_single_scan_id =		61521794;
SmartSelect =			"yes";
Coil 1  (exclude) =		"None";
Uniformity =			"CLEAR";
FOV          AP (mm) =		220;
             RL (mm) =		220;
             FH (mm) =		175;
ACQ voxel size   AP (mm) =	0.649999976;
             RL (mm) =		0.65180105;
             FH (mm) =		1;
Recon voxel size AP (mm) =	0.34375;
             RL (mm) =		0.34375;
             FH (mm) =		1;
Fold-over suppression =		"oversampling";
    L (mm) =			100;
    R (mm) =			100;
Slice oversampling =		"user defined";
    oversample factor =		2;
Reconstruction matrix =		640;
SENSE =				"no";
CS-SENSE =			"yes";
    reduction =			6;
    denoising =			"system default";
k-t Acceleration =		"no";
Stacks =			1;
    slices =			175;
    slice orientation =		"transverse";
    fold-over direction =	"RL";
    fat shift direction =	"P";
Multi-chunk =			"no";
O-MAR =				"no";
Large table movement =		"no";
PlanAlign =			"no";
REST slabs =			0;
Interactive positioning =	"no";
External control =		"no";
Patient position =		"head first";
Patient body position =		"head first";
Patient orientation =		"supine";
Patient body orientation =	"supine";
Scan type =			"Imaging";
Scan mode =			"3D";
    technique =			"SE";
Modified SE =			"no";
Acquisition mode =		"cartesian";
Fast Imaging mode =		"TSE";
    3D VIEW =			"no";
    shot mode =			"multishot";
TSE factor =			53;
    startup echoes =		4;
    profile order =		"linear";
    turbo direction =		"Y";
    DRIVE =			"yes";
    ultrashort =		"no";
    fid reduction =		"strong";
    3D non-selective =		"yes";
Echoes =			1;
    partial echo =		"no";
TE =				"shortest";
Flip angle (deg) =		90;
Refocusing control =		"constant";
    angle (deg) =		45;
    bright fat reduction =	"no";
TR =				"user defined";
    (ms) =			1800;
Halfscan =			"no";
Water-fat shift =		"maximum";
RF Shims =			"fixed";
Shim =				"default";
mDIXON =			"no";
Fat suppression =		"SPIR";
   strength =			"strong";
   frequency offset =		"default";
Grad Rev Fat suppr =		"no";
Water suppression =		"no";
BB pulse =			"no";
MTC =				"no";
APT =				"no";
Custom prepulse =		"no";
MDME =				"no";
Diffusion mode =		"no";
T1 mapping =			"no";
Transmit channels =		"both";
SAR mode =			"high";
B1 mode =			"default";
SAR allow first level =		"no";
PNS mode =			"high";
Gradient mode =			"maximum";
SofTone mode =			"no";
Cardiac synchronization =	"no";
Heart rate > 250 bpm =		"no";
Respiratory compensation =	"no";
Navigator respiratory comp =	"no";
Flow compensation =		"no";
Motion smoothing =		"no";
NSA =				1;
MRE enable =			"no";
CENTRA =			"no";
Manual start =			"no";
Dynamic study =			"no";
Arterial Spin labeling =	"no";
Preparation phases =		"auto";
Interactive F0 =		"no";
Quick Survey =			"default";
B0 field map =			"no";
B1 field map =			"no";
MIP/MPR =			"no";
Images =			"M", (3) "no";
Autoview image =		"M";
Calculated images =		(4) "no";
Reference tissue =		"Grey matter";
Recon compression =		"No";
Preset window contrast =	"soft";
Reconstruction mode =		"real time";
Save raw data =			"yes";
Hardcopy protocol =		"no";
Image filter =			"system default";
Uniformity correction =		"no";
Geometry correction =		"default";
Elliptical k-space shutter =	"default";
Stack Offc. AP (P=+mm) =	10.0683002;
            RL (L=+mm) =	-0.0122832758;
            FH (H=+mm) =	-11.8124113;
      Ang.  AP (deg) =		0;
            RL (deg) =		-0;
            FH (deg) =		-0;
      Free rotatable =		"no";
IF_info_seperator =		1634755923;
Total scan duration =		"17:43.8";
Rel. SNR =			1.56794226;
Act. TR (ms) =			"1800";
Act. TE (ms) =			"261";
ACQ matrix M x P =		"340 x 337";
ACQ voxel MPS (mm) =		"0.65 / 0.65 / 1.00";
REC voxel MPS (mm) =		"0.34 / 0.34 / 1.00";
Scan percentage (%) =		99.1765747;
Act. slice gap (mm) =		0;
WFS (pix) / BW (Hz) =		"2.021 / 215.0";
TSE es / shot (ms) =		"8.4 / 488";
TEeff / TEequiv (ms) =		"261 / 121 ";
Min. TR (ms) =			"509";
Local torso SAR =		"<  8 %";
Whole body SAR / level =	"< 0.3 W/kg / normal";
SED =				"< 0.3 kJ/kg";
Coil Power =			"8 %";
Max B1+rms =			"0.65 uT";
PNS / level =			"76 % / normal";
dB/dt =				"104.9 T/s";
Sound Pressure Level (dB) =	23.897604;

CT Imaging

Parameters:
Helical mode scan from L4 to proximal femur shaft
Slice thickness of 0.625 mm
Kvp = 120

Public workspaceCT and MR Imaging

CT and MR Imaging