3.2 MRI Scan Functional Protocols

This session includes 51 minutes of image acquisition and should be completed in less than one hour of total scan time. This session includes survey scan for head position and positioning image planes subsequent in subsequent scans, a reference can for calibration of the 32 channel SENSE head-coil, a 3D T1 weighted (1,2 or IR Prepped) high-resolution anatomical scan of the entire brain with spatial resolution of 1 x 1 x 1 mm. Functional MRI scanning is done using a special purpose simultaneous ASL/BOLD sequence that will allow activation maps to be computed either from the BOLD data or from the ASL data. Alternatively, quantitative perfusion image data acquired in during language stimulation to be used as a covariate in the analysis of the BOLD data in order to correct for age dependent changes in CBF across the age span of the study cohort from birth to 18 years. In order to accurately quantitate perfusion in each subject, the T1 and transit time measurements from the Physiological Imaging Session are used, along with a measurement of the ASL labeling efficiency made during this Functional Imaging Session. The sequence of scans is tabulated directly below. Details of the key imaging parameters for each sequence are listed in the text that follows. The Table below provides numerical values for key image parameters for each sequence.

Note that the first 5 scans in this series are identical to the first 5 scans described above for the Physiological Imaging Session. Unfortunately these scans must be repeated during this Functional Imaging Session because the subject will not be in the same position. Refer to descriptions for these scans above.


List of Scans in the Functional Session (total length: 50:10.4 )

Scan name Scan length Comments
Survey 00:31.4  
Ref_Head_32 00:44.4  
T1W_3D_IRCstandard32 05:15.5  
EPI-BOLD_NR1 00:10.0  
ASLBOLD_Stories 10:48.0  
ASLBOLD_Sentences 10:48.0 (omitted for children under age 7 years)
HARDI_b3000 11:34.0  












Gradient-echo, single shot EPI acquisition.

This is a typical T2* weighted EPI gradient echo scan used for BOLD-fMRI. In this case we acquire a single time-point with 24 axial slices covering the entire brain. The primary purpose of this scan is to cause the higher order shimming to occur in the selected brain volume and to define this functional volume for use in subsequent EPI based scans for optimal field uniformity. This is a fast scan with the same resolution and field of view that will be used in the baseline CBF measurements. Inspection of this image will be done by the operator to determine whether sufficient homogeneity has been achieved by the shimming process in order to proceed to obtain high quality images. If these images demonstrate distortion or other artifacts, shimming should be repeated or other measures taken to improve the patient positioning and image quality. High order shimming performed to optimize this scan volume should be saved and applied to all subsequent scans in the Physiological Sequence. On the Philips platform this is done by propagating the PB-Volume shim parameter from one scan to the next and preserving the scanning geometry.


Key Imaging Parameters:

Bandwidth EPI:

3313.5 Hz

Acquistion Matrix: 64x64
Total scan time: 10 secs







FOV: (default but can vary for each subject.)
  RL (mm): 240
  AP (mm): 240
  FH (mm): 120
  P-Reduction (AP): 2
Phase Encoding: AP
Reconstructed Matrix: 64x64
Resolution: 3.75x3.75x5
Stacks: 1
Slices: 24
Slice Orientation: Transverse














FA: 90°
TR/TE: 2000 / 35 msec
NSA: 1
Fat Suppression: SPIR
Shim: PB Volume (i.e. highest order shims possible within one vol)







ASL/BOLD Stories and ASL/BOLD Sentences

EPI gradient echo sequence with a PCASL inversion label as follows

These acquisitions represent the key contribution of the Pediatric Functional Neuroimaging Research Network and will provide a novel new set of data from children from birth to age 18. The ASL/BOLD acquisition is a new method that is designed to allow for simultaneous acquisition of an ASL perfusion scan interleaved with a BOLD functional scan within a few hundred milliseconds. The same pCASL arterial tagging pulse train as described above for the baseline CBF measurement is used in this sequence to provide inflow tag at the level below the carotid bifurcation. The 1500 msec labeling sequence is followed 700 msec label by a short echo-time (TE=11 msec) perfusion-weighted single-shot EPI acquisition and then by a BOLD-weighted (TE=35 msec) single-shot EPI acquisition. This sequence is diagrammed below and key imaging parameters are also listed in the table. Note that the ASL and BOLD image volumes are pulled apart in the post-processing stage and statistical parameter maps are formed separately for each image type using the LONI pipeline workflow defined for the project.


This same acquisition strategy is used with two separate functional task acquisitions. In both cases the scans run for 10 min 40 seconds with 64 second blocks alternating between 2 conditions. The tasks themselves are described in more detail in the user manual, section 4.2. Here it is sufficient to state that a series of 160 scans (80 tag/control pairs) are acquired for each task with 16 scans per condition using a TR=4 sec between scans of the same type. The ASL alternates between tagging and control pulses every other scan.




Key Imaging Parameters:

EPI factor: 35
EPI Bandwidth: 3028.5 Hz
Acquisition Matrix: 64x64
Reconstructed Matrix: 64x64
Total scan time: 10 min 48 secs








FOV: (default but can vary for each subject.)
  RL (mm): 240
  AP (mm): 240
  FH (mm): 120
  P-Reduction (AP): 2
  Pos Factor: 1
Phase Encoding: AP 
Resolution: 3.75x3.75x5
Stacks: 1
Slices: 24 
Slice order: Ascend














FAASL: 90°
TR/TEASL/TEBOLD: 4000/11.2/35 msec
Shim: PB Volume (i.e., highest order shims possible within one vol)
NSA: 1
Fat Suppression:  No 








ASL Parameters:

No. of Dynamic Scans: 80 
Label Type: Parallel Slab
Save/Restore Labeling: None 
Label Location:
Label Gap: 20 
Label Duration (msec): 1500 
Post Label Delay: 700 msec = w
Vascular Crushing: No 
FLL pCASL mean B1 amplitude: 1.0mT
FLL pCASL interval: 1.5 ms
FLL pCASL flip angle duration: 0.5 ms
FLL pCASL gradient strength:
FLL pCASL mean gradient: 1
Trigger before Label: Yes














Resting State BOLD

Gradient Echo EPI single shot sequence

This is a typical BOLD-weighted EPI gradient echo scan acquired in the resting state. No task behavior is required and the subject is either asleep or awake with visual fixation on a cross-hair. The EPI Scanning runs continuously with a TR=2 seconds in order to achieve good temporal resolution in the resting state data for connectivity analysis. TE=35 msec in order to yield strong BOLD weighting. A total of 150 scans are acquired with the key imaging parameters as listed below.


Key Imaging Parameters:

EPI Factor: 35 
EPI Bandwidth: 3625.3 Hz
Acquisition Matrix: 80x80
Total scan time: 5 min 08 secs







FOV: (default but can vary for each subject.)
  RL (mm): 240 
  AP (mm): 240 
  FH (mm): 144
  P-Reduction (AP): 2
  Pos Factor: 1
Phase Encoding: AP
Resolution: 3 x 3 x 4
Stacks: 1
Slices: 36
Slice Order: Ascend














FA: 90°
TR/TE: 2000/35 msec
NSA: 1
Dynamic Scans: 150
Fat Suppression: Yes/SPIR/Strong
Shim: PB Volume (i.e., highest order shims possible within one vol)









No. of Dynamic Scans: 150



HARDI-61 Direction

Spin echo EPI single-shot sequence

In this case we use a spin-echo, EPI method with IVIM gradients for diffusion weighting of the scans. Some discussion about spatial resolution vs. angular resolution vs. b-values took place among several of the investigators and consultants in converging to the final parameters for this scan. The proponents of true HARDI scanning advocated for the use of a higher b value for more extreme diffusion weighting (b=3000) in order to allow for probabilistic fiber tractography to resolve crossing fibers.19-22 On the other hand, there are arguments favoring a larger number of diffusion directions in order to be able to resolve crossing fibers from DTI data.23 However, competing against higher b-values and higher angular resolution are the demands of SNR and acquisition time.24 From the literature and discussion with some of those actively using DTI to study early brain development in children we discovered that there are strong arguments in favor of the lowest possible b-value (700-800) for diffusion weighting combined with the highest possible spatial resolution in the EPI data. 25-28  This resulted in an MRI acquisition that was dervired from those distributed by Philips with the 32 channel head coil that makes use of a SENSE factor of 3. In this case, we were able to obtain 2 x 2 x 2 mm spatial resolution with 61 diffusion directions at b=3000 in under 12 minutes. This method was felt to be a good compromise following discussions with Tim Roberts, Paul Thompson, Sususu Mori, Weihong Yuan, and Vince Schmithorst. Seven b=0 images are also acquired at intervals of 8 images apart in the diffusion direction vector. These b0 images are used for corregistration and averaged to form the baseline for solving the diffusion tensor for the eigen values used in quantitative diffusion parameter calculations.


Key Imaging Parameters:

EPI Factor: 39 
EPI Bandwidth: 1752.6 Hz
Acquistion Voxel: 2x2.05x2
Reconstucted Voxel: 2x2x2
Acquisition Matrix: 112x109
No. of directions: 61 plus 7 b0 images = 68
Total scan time: 11 min 34 secs









FOV: (default but can vary for each subject.)
  RL (mm):  224 
  AP (mm):  224 
  FH (mm):  120 
SENSE:  Yes 
  P-Reduction (AP):  3 
  Pos Factor:  1 
Phase Encoding:  AP 
Resolution: 2x2x2
Stacks: 1
Slices: 60
Slice Order: Interleaved (Odd then Even)















FA: 90°
TR/TE: 8112/104 msec
NSA: 1
Fat Suppression: SPIR
Max B-Factor: 3000
Shim: PB Volume (i.e. highest order shims possible within one vol)







Bvalue: 3000

Please see description of the DTI gradient direction calculations and vector provided in the documentation above for the DTI Images acquired as part of the Physiological Protocols.

HARDI Directions: 68 (61 dirs + 7 B0s)

0 -0 0
0.71109 0.52107 0.47206
0.826 -0.104 0.554
0.23604 -0.80915 0.5381
0.66773 0.71271 0.21491
-0.024995 -0.9338 0.35692
-0.52923 0.78034 0.33314
-0.76884 -0.15697 0.61987
0.81113 0.22203 0.54108
0 -0 0
0.2569 0.58576 0.76869
-0.78381 0.16796 0.59786
0.9225 -0.26014 0.28516
0.15601 0.83604 0.52602
-0.063005 0.69105 0.72005
-0.7029 0.50793 0.49793
0.46988 -0.59085 0.65583
-0.86508 -0.37603 0.33203
-0.37903 -0.89208 -0.24602
0 -0 0
0.34893 -0.065987 0.93482
0.046983 0.96764 0.24791
-0.20002 0.86508 0.46004
-0.647 -0.682 0.341
0.035992 0.055988 0.99778
0.25591 0.96465 -0.062977
-0.19801 -0.49501 0.84602
0.5552 -0.74027 0.37914
0.61569 0.082958 0.78361
0 -0 0
-0.31309 0.93827 0.14704
0.58012 -0.81417 0.024005
0.54729 0.41222 0.72839
0.33594 -0.37994 0.86185
-0.35678 -0.85746 0.37077
-0.55676 0.0079965 0.83064
0.73921 -0.45213 0.49914
0.61213 -0.25605 0.74816
-0.67292 -0.46295 0.57693
0 -0 0
0.025007 0.38811 0.92127
-0.78013 0.5951 -0.19303
0.95972 0.077977 0.26992
0.11799 -0.60695 0.78593
-0.99667 0.074975 0.031989
-0.27991 0.17094 0.94469
-0.92149 0.38821 0.012006
-0.41598 -0.65097 0.63497
0.88506 0.40803 0.22402
0 -0 0
0.81379 0.57785 -0.061984
-0.93718 -0.044008 0.34607
-0.967 -0.25 0.049
-0.42401 0.66202 0.61802
-0.55731 0.34019 0.75742
-0.32711 0.9173 -0.22707
0.55276 0.83064 -0.066971
-0.27406 0.4751 0.83617
0.043006 -0.28304 0.95814
0 -0 0
-0.11395 -0.77167 0.62573
-0.76667 0.61573 0.18192
-0.25608 -0.15405 0.9543
0.45876 0.71562 0.52672
0.066027 -0.99641 0.053022
-0.49095 -0.32596 0.80791
0.32397 0.25898 0.90993
-0.90024 0.29408 0.32108


Physiological Imaging Session

Functional Imaging Session



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