Friday, September 2, 2016

multiband acquisition sequence testing: introduction

In the previous couple of posts I shared some strange-looking motion regression curves, which turned out to be related to respiration. I also posted examples of average voxel timecourses which I've been looking at to get a feel for the task-related signal in these images, and how it might be impacted by the respiration-related oscillations. Task-related signal is of primary importance to us (e.g., MVPA and FIR analyses), and ideally analysis of single events. So, everything here is through that lens; implications for resting state, functional connectivity analyses, etc. are likely very different, and I'm not going to speculate on that at all.

We've done a lot of analyses this week, and people have been kind enough to share some of their data and thoughts. This is a lot of material and fairly preliminary, but I think will be of great interest to people using multiband sequences and/or HCP data, so I'll put a few posts together, rather than trying to fit everything into one.

Last Sunday we ran a series of test scans, using as participant the lab member with the most prominent oscillations (examples of which are shown here), and the HCP MOTOR task. This task is short (just over 3.5 minutes long), and has blocks of right or left hand movement, right or left foot movement, and tongue movement. I showed example timecourses from the HCP in the previous post; the graphs from our test runs (see this post) are the same, except that I color-coded the task blocks by body type for easier visibility.

We ran three main test sequences, plus a few variations. Acquisition details are below the fold. The three main sequences were:
  • MB8: The same multiband 8 sequence we've been using (described here), except with LeakBlock enabled. TR = 800 msec, acquired voxels 2 x 2 x 2 mm.
  • MB4: A new (for us) multiband 4 sequence. TR = 1200 msec, acquired voxels 2.4 x 2.4 x 2.4 mm.
  • MB0: A control, non-multiband sequence, the ep2d_bold built-in scanner sequence.TR = 2500 msec, acquired voxels 4 x 4 x 4 mm.
Preprocessing was through the HCP pipelines for the multiband sequences, through SPM12 for the control (realignment and spatial normalization; voxels resampled to 3x3x3); motion regressors plotted (here) are as generated by those programs. I generated voxel timecourses as described before, using afni and the Gordon parcellation for ROIs. We have respiration belt recordings for the multiband sequences, but not for the control.

The functional images we collected with the multiband acquisitions are beautiful. The screenshot above shows a frame from an AP run of each type (the second left-hand movement block, to be precise), before (top) and after (bottom) preprocessing. The MB8 functional images practically look like anatomical images, there's so much detail.

The next few posts will get into the respiration and activity timecourses we found in each.

acquisition details for MB4 and MB0 below the jump; see the previous post for MB8.



MB4 scanning details

Series description fMRI_AP_2p4mm_MB4_tr1150_te33_MOTOR
Sequence epfid2d1_90
Frames 184
Acquisition type 2DScan sequence EP
Sequence variant SK\SS
Scan options FS\EXT
Field Strength 3.0
Voxel resolution. 2.4000000953674, 2.4000000953674, 2.4000000953674
FOV 720 x 720
Orientation Tra
Subject position HFS
TR 1200.0
TE 33.0
Flip 63
Echo Spacing (sec) 5.900122722552628E-4
Readout sample spacing 2500.0
Pixel bandwidth 2220.0
PhaseEncoding direction positve 1
In-plane phase encoding direction COL
In-plane phase encoding rotation 0.103672557568
Siemens Orientation Text Tra>Cor(-23.9)>Sag(4.5)
Siemens Table Position 0\0\0
Siemens GRADSPEC lOffset \\
Siemens GRADSPEC alShimCurrent 489\-4\6\51\1
HCP MB Recon Location 1
Siemens Mosaic Slice Count 60
Siemens iPAT factor 1
Siemens txRefAmp 250.138641357
Siemens Coil String HEA;HEP
Siemens sWipMemBlock.alFree[0] 4105
Siemens sWipMemBlock.alFree[9] 3
Siemens sWipMemBlock.alFree[10] 10
Siemens sWipMemBlock.alFree[13] 4
Siemens sWipMemBlock.alFree[16] 1
Siemens sWipMemBlock.alFree[21] 40000
Siemens sSliceArray.asSlice[0].dThickness 2.4
Siemens sSliceArray.asSlice[0].dPhaseFOV 216.0
Siemens sSliceArray.asSlice[0].dReadoutFOV 216.0
Siemens sSliceArray.asSlice[0].dInPlaneRot 0.103672557568
Siemens sSliceArray.asSlice[0].sPosition.dSag 3.2292030568
Siemens sSliceArray.asSlice[0].sPosition.dCor -42.4110059219
Siemens sSliceArray.asSlice[0].sPosition.dTra -73.5158695831
Siemens sSliceArray.asSlice[0].sNormal.dSag -0.07818081918
Siemens sSliceArray.asSlice[0].sNormal.dCor 0.4036100151
Siemens sSliceArray.asSlice[0].sNormal.dTra 0.9115847274
Siemens sAdjData.sAdjVolume.dThickness 144.0
Siemens sAdjData.sAdjVolume.dPhaseFOV 216.0
Siemens sAdjData.sAdjVolume.dReadoutFOV 216.0
Siemens sAdjData.sAdjVolume.dInPlaneRot 0.103672557568
Siemens sAdjData.sAdjVolume.sPosition.dSag -2.30599894114
Siemens sAdjData.sAdjVolume.sPosition.dCor -13.8354168528
Siemens sAdjData.sAdjVolume.sPosition.dTra -8.97567088321
Siemens sAdjData.sAdjVolume.sNormal.dSag -0.07818081918
Siemens sAdjData.sAdjVolume.sNormal.dCor 0.4036100151
Siemens sAdjData.sAdjVolume.sNormal.dTra 0.9115847274
fMRI_Version_Sequence ve11b/master r/93e61f0; Jul 21 2016 00:18:29 by eja
fMRI_Version_ICE_Win32 ve11b/master r/93e61f0; Jul 21 2016 00:10:54 by eja
fMRI_Version_ICE_Linux ve11b/master r/93e61f0; Jul 21 2016 05:12:38 by eja


"MB0" scanning details

Series description ep2d_bold_moco_sensory
Sequence *epfid2d1_64
Frames 84
Acquisition type 2DScan sequence EP
Sequence variant SK
Scan options FS
Field Strength 3.0
Voxel resolution. 4.0, 4.0, 4.0
FOV 384 x 384
Orientation Tra
Subject position HFS
TR 2500.0
TE 27.0
Flip 83
Echo Spacing (sec) 5.90001132802175E-4
Readout sample spacing 4100.0
Pixel bandwidth 1905.0
PhaseEncoding direction positve 1
In-plane phase encoding direction COL
In-plane phase encoding rotation 0.0706858347058
Siemens Orientation Text Tra>Sag(6.3)>Cor(-3.8)
Siemens Table Position 0\0\0
Siemens GRADSPEC lOffset \\
Siemens GRADSPEC alShimCurrent 449\-28\-34\83\-18
Siemens Mosaic Slice Count 34
Siemens iPAT factor 1
Siemens txRefAmp 250.138641357
Siemens Coil String HEA;HEP
Siemens sSliceArray.asSlice[0].dThickness 4.0
Siemens sSliceArray.asSlice[0].dPhaseFOV 256.0
Siemens sSliceArray.asSlice[0].dReadoutFOV 256.0
Siemens sSliceArray.asSlice[0].dInPlaneRot 0.0706858347058
Siemens sSliceArray.asSlice[0].sPosition.dSag 5.31226658729
Siemens sSliceArray.asSlice[0].sPosition.dCor -21.6531024667
Siemens sSliceArray.asSlice[0].sPosition.dTra -80.2066039275
Siemens sSliceArray.asSlice[0].sNormal.dSag -0.1087323357
Siemens sSliceArray.asSlice[0].sNormal.dCor 0.06708937544
Siemens sSliceArray.asSlice[0].sNormal.dTra 0.9918045649
Siemens sAdjData.sAdjVolume.dThickness 136.0
Siemens sAdjData.sAdjVolume.dPhaseFOV 256.0
Siemens sAdjData.sAdjVolume.dReadoutFOV 256.0
Siemens sAdjData.sAdjVolume.dInPlaneRot 0.0706858347058
Siemens sAdjData.sAdjVolume.sPosition.dSag -1.86406756891
Siemens sAdjData.sAdjVolume.sPosition.dCor -17.2252036877
Siemens sAdjData.sAdjVolume.sPosition.dTra -14.7475026441
Siemens sAdjData.sAdjVolume.sNormal.dSag -0.1087323357
Siemens sAdjData.sAdjVolume.sNormal.dCor 0.06708937544
Siemens sAdjData.sAdjVolume.sNormal.dTra 0.9918045649

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