Hi Rito shortening the TE wouldn't change the overall acquisition. If it's total brain volume you are interested in, you might consider getting the low flip FLASH in addition
cheers Bruce On Tue, 10 Dec 2013, Ritobrato Datta wrote: > Hi Bruce, > > Thank you for the reply and the suggestions. So if I shorten the TE on the > FLASH and lengthen the overall scan time, will that help ? I am specifically > interested in the brain vol (minus CSF) for MS atrophy as well as cortical > thickness analyses so I am keen to explore the possibility to extract both > the measures from a single anatomical sequence. > > Please let me know. > > Thanks > > Rito > > ----- Original Message ----- > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > To: Ritobrato Datta <rida...@mail.med.upenn.edu> > Cc: free surfer <freesurfer@nmr.mgh.harvard.edu> > Sent: Tue, 10 Dec 2013 13:42:05 -0500 (EST) > Subject: Re: [Freesurfer] T1 FLASH parameters for cortical thickness analyses > > 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 >> >> >> > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
