Hi Andre,
I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...", not the ones I am using/planning to adjust.
Thanks,
Jelmer
________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study
no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Bruce and Andre,
PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine...
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.kok02@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre,
Many thanks for your comments!
Cheers,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Andre van der Kouwe [andre@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
No, I think that's a reasonable protocol to use and good to use SENSE to speed it up.
-------- Original message -------- From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study
looks pretty reasonable. Andre: any comments/suggestions?
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Hi Bruce,
Thanks for your fast reply.
Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient).
Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_pro...":
" Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE "
suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is
missing in our protocol that is the most important difference?)
Thanks,
Jelmer
Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl
[fischl@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study
Hi Jelmer
if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc....). We also have recommended morphometry sequences on our website.
10 min is a pretty long structural scan for a modern MRI scanner.
cheers Bruce
On Tue, 1 Apr 2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts, We are planning to start a new MRI study which will include T1 scans. As we are in a testing phase now, I was wondering whether you could comment on the attached screenshots. Clearly, "scan1" has a better white matter/grey matter contrast than "scan2". Do you think going for "scan1" would be the sensible thing to do when we later wish to use Freesurfer with these scans? Or perhaps is neither of the examples I attached good enough?
By the way, these scans were acquired on a Philips 3T scanner, both taking around 10 minutes.
It you need any more information, please let me know. Many thanks in advance for your advice.
Jelmer Kok
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