Hi Reem,
I have no skyra experiences but:
- registration of T1-w MPRAGEs into standard space does usually not suffer from iPAT
- FIRST, VBM & FreeSurfer may be better off without acceleration. a crucial parameter is the TE as it determines how bright the dura comes out.
- if you use iPAT for the strucs, try to use more reference lines (i.e. >48, e.g. 72)
EPI:
yes, you loose signal but you reduce the effective echo spacing, i.e. the distortions, by the iPAT factor and you may be able to increase the resolution of your scans to something like 1.5mm isotropic AND keep your TE around 30ms.
but again, you loose signal and may need a 32 channel head coil, for example (not sure if the skyra supports it)
field maps:
the crucial parameter is the TE difference. every system is different, and usually you don't even operate at exactly 3T (but 2.96, for example). the 'best' TE difference depends on the fat-water shift and you may want to adjust this to your precise system (note that the skyra is more prone to inhomogeneities than the trio, for example). however, having said this you may well stick to the siemens default as it won't make >much< of a difference for the unwarping.
if you go for iPAT, use GRAPPA and not mSENSE on the siemens (bold statement but a rough guideline).
hth,
andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Reem Jan [[log in to unmask]]
Gesendet: Mittwoch, 27. Juli 2011 03:49
An: [log in to unmask]
Betreff: [FSL] Scanner aquisition parameter queries - parallel imaging and field maps
Dear FSLers
I’m in the process of setting up a new trial and trying to decide on acquisition parameters, particularly regarding parallel imaging (iPAT) and field maps.
We will be using a Siemens Skyra 3T MRI system, and acquiring EPIs for task fMRI and DTI as well as T1-weighted MPRAGE sequences. For iPAT we have the options of using GRAPPA or mSENSE. The default is GRAPPA.
MPRAGE
I researched the pros and cons of turning iPAT on and it seems that it would reduce acquisition time for the MPRAGE (in the case of our scanner down from 8:57 mins to 4:52 mins), however when iPAT is turned on (acceleration factor: 2), the SNR also drops from 1.41 to 1.
I plan to use the MPRAGE structural scans for VBM and FIRST analyses:
· Would it be okay for parallel imaging to be turned on?
· What voxel size would you recommend? In the past I have used 1x1x1mm. Is there a benefit to using smaller voxels (e.g. 0.9x0.9x0.8mm)?
EPI
I realise that the acquisition time of EPIs is unaffected by iPAT, however, it is meant to improve geometric distortion around air pockets etc, but the radiographer also told me that I can lose up to 30% of the signal.
· I’m having trouble deciding whether to leave iPAT turned off for the DTI and fMRI sequences in order to maximise SNR, but have the risk of increased distortion. I was hoping to draw on your expertise on whether this trade-off is worthwhile?
Field maps
For the new trial I want to ensure that I acquire field maps for the fMRI dataset as per Mark Jenkinson’s advice at the FSL course and on the FSL mailing list.
· Are there any specific considerations or would the built-in scanner parameters be okay?
Examples
· Lastly, I have some MPRAGE and EPI images from a pilot, that have been acquired with iPAT turned on, and wondered (if it’s not too much trouble) whether I can upload examples of these so the FSL experts could tell me if their quality is good enough for me to proceed without changes.
Many thanks in advance, your advice is much appreciated.
Best regards
Reem
Reem Jan
BPharm (Hons), RegPharmNZ
PhD Student / Pharmacist
School of Pharmacy, Faculty of Medical & Health Sciences,
The University of Auckland, Private Bag 92019,
Auckland, New Zealand.
Ph: +64 9 373 7599 ext 88468. DDI: +64 9 923 8468
F: +64 9 367 7192
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