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 fischl@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@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 -
Can I get reliable cortical thickness estimates using a T1 3D FLASH sequence at 3T Siemens TRIO ?
Which version of freesurfer is recommended ?
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 ?
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 ?
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
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