[[TableOfContents]]

= CBU default imaging sequences =
== Introductory note ==
The sequences shown on this page are meant to be used as guidelines, but they can be modified in order to meet the needs of your study. If you would like some advice on setting up your sequence, please contact Marta Correia ( marta.correia@mrc-cbu.cam.ac.uk ).

Here attachment:NewSequences.ppt you can find an overview of the sequences which have recently been implemented in our scanner.

If you want to double check what parameters were used for images already acquired, you can also look at the information from the DICOM headers, which SPM saves when converting to Nifti format.  After DICOM conversion every folder has a dicom_headers.mat file.  In Matlab:

{{{
>> load dicom_headers.mat >> DICOMHEADERS{1} }}}
will let you check the parameters for the images you've acquired.

== CBU_EPI ==
For fMRI
|| Description || Standard EPI sequence for fMRI ||
|| Acquisition time || 2 s (per volume) ||
|| Type || 2D ||
|| Slices || 32 ||
|| Slice gap || 25% ||
|| Slice thickness || 3 mm ||
|| Slice order || Descending (32,31,...,1) ||
|| FOV || 192 mm  x  192 mm ||
|| Matrix || 64  x  64 ||
|| Resolution || 3 mm  x  3mm ||
|| TR || 2000 ms ||
|| TE || 30 ms ||
|| Flip angle || 78 deg ||
|| Bandwidth || 2232 Hz/Px ||
|| Echo spacing || 0.51 ms ||


=== Trigger pulse timing ===
To within a few ms, the stimulus delivery trigger pulse happens 35 ms before the acquisition of the first scan (centre of k space) of each volume. Note there is a latency of 20 ms in the visual display. The trigger pulse length is 1 ms.

== CBU_SilentEPI ==
Schmitter et al, Magn Reson Mater Phy (2008) 21:317–325.

Peelle JE, Eason RJ, Schmitter S, Schwarzbauer C, Davis MH (2010) Evaluating an acoustically quiet EPI sequence for use in fMRI studies of speech and auditory processing. NeuroImage. http://dx.doi.org/10.1016/j.neuroimage.2010.05.015

See UsingTheSilentSequence for discussion.
|| Description || Quiet echo-planar imaging for auditory FMRI ||
|| Acquisition time || 2.64s (per volume) ||
|| Type || 2D ||
|| Slices || 32 ||
|| Slice gap || 25% ||
|| Slice thickness || 3 mm ||
|| Slice order || Descending (32,31,...,1) ||
|| FOV || 192 mm  x  192 mm ||
|| Matrix || 64  x  64 ||
|| Resolution || 3 mm  x  3mm ||
|| TR || 2640 ms ||
|| TE || 44 ms ||
|| Flip angle || 83 deg ||
|| Bandwidth || 1220 Hz/Px ||


== CBU_MEPI ==
The multi-echo sequence was developed by Benedikt Poser and colleagues at the FC Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands. A comparison between multi-echo and standard fMRI acquisition can be found here http://onlinelibrary.wiley.com/doi/10.1002/mrm.20900/pdf .
||Description ||Echo planar imaging at multiple echo times ||
||Acquisition time || 2.47s (per volume) ||
|| Type || 2D ||
||Slice ||32 ||
||Slice gap ||25% ||
||Slice thickness ||3mm ||
||Slice order ||Descending (32,31,...,1) ||
|| FOV || 192mm  x 192mm ||
|| Matrix || 64 x 64 ||
|| Resolution || 3mm x 3mm ||
|| TR || 2470ms ||
|| TE ||9.4ms, 21.2ms, 33ms, 45ms, 57ms ||
|| Flip angle || 83 deg ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 3 [[BR]] Reference lines PE: 24 ||


== CBU_3DEPI ==
|| Description || 3D fast imaging sequence for high resolution fMRI ||
|| Acquisition time ||1.508 s /  1.060 s / 1.326 s (per volume) ||
|| Type || 3D ||
||Slices ||40 / 30 / 20 ||
||Slice gap ||0% ||
||Slice thickness ||1.5mm / 2mm / 3mm ||
||Slice order ||Interleaved ||
|| FOV || 192 mm x 192 mm ||
|| Matrix || 192x192 / 128x128 / 96x96 ||
|| Resolution || 1.5mmx1.5mm / 2mmx2mm / 3mmx3mm ||
|| TR || 58 ms / 53 ms / 51 ms ||
|| TE ||30 ms ||
|| Flip angle || 16 deg / 15 deg / 15 deg ||
||Bandwidth ||1628 / 2228 / 2228 Hz/Px ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2x2 [[BR]] Reference lines PE: 40x40 ||

== CBU_MPRAGE ==
|| Description || High-resolution structural MRI ||
|| Acquisition time || 4 min 32s ||
|| Type || 3D ||
|| FOV || 256 mm  x  240 mm  x 192mm ||
|| Matrix || 256  x  240  x192 ||
|| Resolution || 1 mm isotropic ||
|| TR || 2250 ms ||
|| TI || 900 ms ||
|| TE || 2.99 ms ||
|| Flip angle || 9 deg ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2 [[BR]] Reference lines PE: 24 ||

== MGH_MEMPRAGE ==
|| Description || Multi-echo high resolution structural MRI (4 echoes)||
|| Acquisition time || 6min 3s ||
|| Type || 3D ||
|| FOV || 256 mm  x 256mm  x 192mm ||
|| Matrix || 256  x 256 x 192 ||
|| Resolution || 1 mm isotropic ||
|| TR || 2530 ms ||
||TI||1200 ms||
|| TE || 1.64 / 3.5 / 5.36 / 7.22 ms||
|| Flip angle || 7 deg||
|| Bandwidth || 651 Hz/Px ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2 [[BR]] Reference lines PE: 32 ||
== CBU_T2 ==
|| Description || High-resolution T2-weighted structural MRI ||
|| Acquisition time || 4 min 30s ||
|| Type || 3D ||
|| FOV || 256 mm  x  240 mm  x 192mm ||
|| Matrix || 256  x  240  x192 ||
|| Resolution || 1 mm isotropic ||
|| TR || 2800 ms ||
|| TE || 408 ms ||
|| Flip angle || 90 deg ||
||Bandwidth ||751 Hz/Px ||
||Echo spacing ||3.36 ms ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2 [[BR]] Reference lines PE: 24 ||
== CBU_TSE ==
|| Description || T2-weighted structural MRI ||
|| Acquisition time || 1 min 38 s ||
|| Slices || 29 ||
|| Slice gap || 30% ||
|| Slice thickness || 4 mm ||
|| Type || 2D ||
|| FOV || 220 mm  x  220 mm ||
|| Matrix || 320  x  320 ||
|| Resolution || 0.7 x 0.7 mm ||
|| TR || 5060 ms ||
|| TE || 102 ms ||
|| Flip angle (refoc. pulse) || 140 deg ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2 [[BR]] Reference lines PE: 26 ||
== CBU_Fieldmapping ==
|| Description || Magnetic field mapping sequence. Required for [[BR]] - undistortion of fMRI data [[BR]] - functional sensitivity mapping ||
|| Acquisition time || 54 s ||
|| Type || 2D ||
|| Slices || 32 ||
|| Slice gap || 25% ||
|| Slice thickness || 3 mm ||
|| FOV || 192 mm   x  192 mm ||
|| Matrix || 64 x 64 ||
|| Resolution || 3 mm   x  3 mm ||
|| TR || 400 ms ||
|| TE || 5.19 ms / 7.65 ms ||
|| Flip angle || 60 deg ||
== CBU_DTI_InLea_2x2x2 ==
|| Description || Standard sequence for diffusion MRI. [[BR]] - isotropic voxel resolution [[BR]] - interleaved slice acquisition ||
|| Acquisition time || 8min 52s / 9min 33s ||
|| Type || 2D ||
|| Slices || 63 / 68 ||
|| Slice gap || none ||
|| Slice thickness || 2 mm ||
|| Slice order || Interleaved ||
|| FOV || 192 mm   x  192 mm ||
|| Matrix || 96 x 96 ||
|| Resolution || 2 mm   x  2 mm ||
|| TR || 7800 ms / 8400 ms ||
|| TE || 90 ms ||
|| Diff directions || 64 ||
|| Diff weightings || 2 ||
|| b-value1 || 0 s/mm2 ||
|| b-value2 || 1000 s/mm2 ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 2 [[BR]] Reference lines PE: 40 ||
For more information on the diffusion MRI sequence go to AnalyzingDiffusion. If you have an ongoing study or wish to compare your results with data that you had previously acquired, the old standard CBU sequence for diffusion imaging (CBU_DTI_64D_1A) will still be available to be used.

== CBU_GQI_101 ==
|| Description || High angular resolution diffusion MRI sequence for GQI analysis ||
|| Acquisition time || 14min 21s ||
|| Type || 2D ||
|| Slices || 55 ||
|| Slice gap || none ||
|| Slice thickness || 2.5 mm ||
|| Slice order || Interleaved ||
|| FOV || 240mm   x  240mm ||
|| Matrix || 96 x 96 ||
|| Resolution || 2.5 mm   x  2.5 mm ||
|| TR || 8200 ms ||
|| TE || 69 ms ||
|| Diff directions || 101 ||
|| Diff weightings || multiple ||
|| max b-value || 4000 s/mm2 ||
|| flip angle || 90 deg ||
|| Bandwidth || 2004 Hz/Px ||
|| Parallel imaging || GRAPPA [[BR]] Acceleration factor PE: 3 [[BR]] Reference lines PE: 40 ||
== CBU_MTI ==
|| Description || Magnetization Transfer Imaging ||
|| Acquisition time || 2 x 2min 36s ||
|| Type || 3D ||
|| Slices || 84 ||
|| Slice gap || 0% ||
|| Slice thickness || 1.5 mm ||
|| Slice order || Interleaved ||
|| FOV || 192 mm  x  192 mm ||
|| Matrix || 128 x  128 ||
|| Resolution || 1.5 mm  x  1.5mm ||
|| TR || 30 ms ||
|| TE || 5 ms ||
|| Flip angle || 12 deg ||
|| Bandwidth || 190 Hz/Px ||
== CBU_SWI ==
||Description ||Susceptibility Weighted Imaging to image vessels and veins in the brain ||
|| Acquisition time || 6min 38s ||
|| Type || 3D ||
|| Slices || 72 ||
|| Slice gap || 0% ||
|| Slice thickness || 1.2 mm ||
|| Slice order || Interleaved ||
|| FOV || 230mm  x  178mm ||
|| Matrix || 448 x  381 ||
|| Resolution || 0.6 mm  x  0.5 mm ||
|| TR || 28 ms ||
|| TE || 20 ms ||
|| Flip angle || 15 deg ||
|| Bandwidth || 120 Hz/Px ||