Hi Ri the sequence looks reasonable, although your TE of 5ms is somewhat long and will reduce CNR and SNR. Can you shorten it? I would think you should be able to. We looked at this for a while, and in the end the mprage outperformed FLASH in terms of cortical gray matter/cerebral white matter CNR/unit time. The FLASH scans were ok, but not as good as mprage. I think either is fine for ICV, although if you collect a lower fiip FLASH which will be PD weighted (e.g. a 5deg) then that will be an advantage for ICV.
cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: > Hi All, > > I have collected T1 3D FLASH on a subject and here are some details of the > sequence, > > Manufacturer = SIEMENS > StudyDescription = Neuro_3T^brain_3t > SeriesDescription = Axial Global FLASH FA27 > ManufacturersModelName = Verio > ReferencedImageSequence = > 1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005978\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005980\1.2.840.10008.5.1.4.1.1.4\1.3.12.2.1107.5.2.36.40156.30000013112219461598300005979 > ScanningSequence = GR > SequenceVariant = SP > ScanOptions = SAT1 > MRAcquisitionType = 3D > SequenceName = *fl3d1 > SliceThickness = 1 > RepetitionTime = 20 > EchoTime = 5 > InversionTime = - > NumberofAverages = 1 > ImagingFrequency = 123.200338 > ImagedNucleus = 1H > EchoNumbers = 1 > MagneticFieldStrength = 3 > NumberofPhaseEncodingSteps = 192 > EchoTrainLength = 1 > PercentSampling = 100 > PercentPhaseFieldofView = 75 > PixelBandwidth = 179 > DeviceSerialNumber = 40156 > SoftwareVersions = syngo MR B17 > ProtocolName = Axial Global FLASH FA27 > TransmitCoilName = Body > AcquisitionMatrix = 0\256\192\0 > In-planePhaseEncodingDirection = ROW > FlipAngle = 27 > VariableFlipAngleFlag = N > SAR = 0.19411263 > > My questions are the following - > > 1) Can I get reliable cortical thickness estimates using a T1 3D FLASH > sequence at 3T Siemens TRIO ? > > 2) Which version of freesurfer is recommended ? > > 3) One reason, I collected T1 FLASH is I want to get whole brain volume and > brain parenchymal fraction in Multiple sclerosis patients. But if freesurfer > prefers MPRAGES over FLASH for cortical thickness, I am wondering how > reliable are the standard MPRAGE sequences for calculation of whole brain > volume and brain parenchymal fractions ? > > 4) I ran the recon on the FLASH using freesurfer 5.3 and it looks very decent > but has anyone tested and optimized the parameters for the T1 FLASH sequence > for cortical thickness estimations ? > > 5) If you can share your opinion and experiences in this topic and maybe > point me to some references using flash and freesurfer for cortical > thickness, that will be very helpful. > > Best > > Ri > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
