I can't think of a good reason that you would want to have nonisotropic
resolution for tractography if you have the choice to avoid it. You will
have worse partial volume effects in the Z direction with 0.87 x 0.87 x 3
than 2.5x2.5x2.5 leading to potentially biased results. It makes the most
sense to go as low as you can with the slice thickness as far as scan time
is concerned and then set the inplane resolution to the same to maximize
SNR. If you are worried about partial voluming and are willing to sacrifice
SNR/increase scan time, scan at 2x2x2mm.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Adil Javed
Sent: Thursday, March 04, 2010 11:42 PM
To: [log in to unmask]
Subject: Re: [FSL] DTI question
Hi,
thanks for the quick response.
So if I turned off the interpolation and just acquired DTI imaging at 0.87 x
0.87 x 3 with 32 directions and 1 average, would this take too long to scan?
Wouldn't this resolution work for tractography as well? Is 2.5 x 2.5 in
plane resolution suggested to cut down on the scan time? wouldn't higher
resolution scans avoid partial volume effects and EPI-related distortions.
also, what program do you use to average separate 4D DTI volumes?
Thanks so much for your helpful comments,
AJ
--- On Thu, 3/4/10, Matt Glasser <[log in to unmask]> wrote:
> From: Matt Glasser <[log in to unmask]>
> Subject: Re: [FSL] DTI question
> To: [log in to unmask]
> Date: Thursday, March 4, 2010, 9:32 PM
> If you are wanting to do tractography
> I would think you would want at least
> 30 directions and 2.5x2.5x2.5mm resolution. 2x2x2mm
> resolution would be
> better, but perhaps harder to get at 1.5T with reasonable
> SNR and a
> reasonable amount of averages (i.e. scan time). You
> should acquire your
> diffusion averages separately (not average on the scanner),
> and you should
> not have any interpolation turned on.
>
> How much scan time you have will determine how many
> averages and how many
> directions you can get, but it is better to acquire more
> unique directions
> rather than more averages (i.e. one average of 60
> directions is better for
> tractography than 2 averages of 30 directions).
>
> At 3T, it is definitely worth correcting your data for EPI
> distortion with a
> field map, however perhaps this is somewhat less important
> at 1.5T as the
> distortion is less.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf
> Of Adil Javed
> Sent: Thursday, March 04, 2010 9:23 PM
> To: [log in to unmask]
> Subject: [FSL] DTI question
>
> Hi,
> I am acquiring DTI images on our Phillips 1.5 T. I
> need to overlay T2 scans
> on DTI to get lesion and non-lesion MD/FA/tractography
> info. My questions
> are:
> 1-I am acquiring DTI images in 32 directions, b=1000, only
> 1 4D volume,
> acquired in plane resolution of 0.87 x 0.87 with 3 mm slice
> thickness. The
> reconstructed dimensions are 2.5mm x 2.5mm x 3mm.
> Reconstructed Voxel
> resolution 256 x 256 x 60. Does this sound
> reasonable? I have seen other
> publications acquire DTI at 2-to-3 x 2-to-3 x 5-to-6mm?
> with voxel
> resolution of 90-128 x 90-128? Not sure if this too low of
> a resolution.
> can anyone comment on this? What are advantages or
> disadvantages of lower vs
> higher acquired resolutions? Also, some use an
> average of 3-9 images per
> slice. Any advantage of this, b/c the scan time would
> be huge.
>
> many thanks in advance,
> aj
>
>
>
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