Hi Burkhard,
Thanks so much for your advice.
I just set up the DTI protocol on our 3T Phillips MRI.
As you suggested,
Voxel size 2x2x2 mm^3
FOV 224 x 224
Acquired matrix 112 x 112, which is reconstructed to 256 x 256. You were right, the size of this single acquisition, 32 directions is 312MB. But, FSL can handle it, just takes a long time.
The reason I wanted 112 x 112 data recon to 256x 256 matrix is that I want to overlay FLAIR and T1 images with resolutions of 256 x 256 on top of DTI data for lesion analysis.
What do you think about others who say not to interpolate the data on the scanner from low resolution such as 112 x 112 to high resolution such as 256x256?
Thanks for your help,
adil
--- On Thu, 3/11/10, Burkhard Mädler <[log in to unmask]> wrote:
> From: Burkhard Mädler <[log in to unmask]>
> Subject: Re: [FSL] DTI imaging
> To: [log in to unmask]
> Date: Thursday, March 11, 2010, 6:08 AM
> Hi Adil,
> From the scan parameters you mentioned it is not possible
> to get an reconstructed
> isotropic dataset with 2x2x2 mm^3.
> I just set it up in the Philips MR-simulator. With a
> FOV=240 and an acquisition
> matrix of 120x118 you cannot reconstruct the data in the
> same matrix size because
> of FFT-issues. The recon size of your data need to be
> multipliers of 16, therefore the
> reconstructed matrix can only be:
> 96x96, 112x112, 128x128 and so on.
> If you want to achieve an iso-resolution of 2x2x2mm^3 in
> your recon-data you have to
> change your FOV or accept a larger voxel size,e.g.:
> voxel-size: 2x2x2mm^3
> matrix: 112X112 or 128x128
> FOV: 224x224cm or 256x256cm
>
> as you see, you only have two practical choices to achieve
> an iso 2x2x2, either FOV=224
> or FOV=256 unless you slightly increase your voxel size.
> With single shot EPI acquisition this decision is difficult
> to make. EPI-images tend to
> get more distorted as longer the read-out train gets.
> Aiming for a 128 matrix is pushing
> the envelope for single shot EPI-DTI. On the other hand you
> also lose a lot of signal
> because with a longer EPI-readout train your effective TE
> needs to be longer, hence
> less signal due to T2*-decay.
>
> Without knowing more about your study purpose it is very
> difficult to give advice
> remotely.
>
> To your second question:
> you never lose information by reconstructing images to
> higher (!) resolution but there
> are other issues to consider:
> - for fiber tracking a non-isotropic voxel size is not
> recommended.
> - the amount of memory you need for postprocessing grows
> very fast with interpolated
> data,e.g.
> 60 slices DTI-high (32 directions) with 128x128
> matrix = ca. 65MByte
> 60 slices DTI-high (32 directions) with 256x256
> matrix = ca. 260 MByte
>
> for some fiber tracking programs the later one can become
> already a challange!
>
> Cheers,
> Burkhard.
>
> Burkhard Mädler, PhD
> Tel.: (+49) 228 287 16186
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
> On Behalf Of Adil Javed
> Sent: Thursday, March 11, 2010 1:20 AM
> To: [log in to unmask]
> Subject: [FSL] DTI imaging
>
> Hi,
> for those who are experts in DTI:
> I am acquiring DTI images on 3.0T Phillips scanner using 32
> directions, FOV 240, acquired matrix is 120 x 118 with
> acquired voxel dimensions of 2x2x2.
> In order to overlay DTI FA/MD/ or tracts on a FLAIR or T1
> image, I need to reconstruct the matrix to 256 with voxel
> RECON to 0.94 x 0.94 x 2 so they align with my FLAIR
> or T1 images.
>
> Question: is this ok or do you see any problems with
> this approach? By reconstructing voxels down to 0.94 x
> 0.94 x 2
> after they are Acquired in 2x2x2 size, am I losing any
> information?
>
> many thanks for your help.
>
> adil
>
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