The data is from a 2d EPI sequence converted from DICOM with mrtrix
routines.
>From mri_info I get:
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
3.8554
: x_a = 0.0000, y_a = -0.9285, z_a = -0.3714, c_a =
-7.2492
: x_s = 0.0000, y_s = -0.3714, z_s = 0.9285, c_s =
15.6468
Orientation : LPS
Primary Slice Direction: axial
The issue is then with the DICOM conversion?
Thx,
-Maarten
On Wed, Oct 19, 2016 at 3:39 PM, Harms, Michael <[email protected]> wrote:
>
> Is your DWI data by any chance saved with an orientation other than LAS or
> RAS?
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: [email protected]
>
> From: <[email protected]> on behalf of Maarten
> Vaessen <[email protected]>
> Date: Wednesday, October 19, 2016 at 6:50 AM
> To: "[email protected]" <[email protected]>
> Subject: [HCP-Users] alignment issues with diffusion data
>
> Hello experts,
>
> I have been trying to use the HCP Diffusion preprocessing pipeline for my
> own diffusion data. However, I run into a lot of issues at the final stage
> of the pipeline where the dwi data is registered to the T1w_acpc space (the
> freesurfer part of the pipeline runs fine on the structural images, the
> eddy correction also seems to run fine).
> So far I have not had a single subject where this alignment went smoothly
> and was accurate.
> It seems to be a problem with flirt. In the DiffusiontoStructural.sh
> subscript there are several calls to flirt (or epi_ref_dof) with the T1 as
> reference and for some reason flirt gives very wrong results like AP
> inverted or cerebellum to frontal lobe matching etc...
> I have managed to solve some cases with a call to only flirt and not
> epi_reg_dof and adding -useqform to the flirt options, but some I only
> managed by doing a rough manual alignment first. When the initial reg to T1
> in ok-ish the bbregister and later parts all work very well.
> I don't think my dwi data is very special (1.5 mm^3 90 dir 2 shell), so I
> have no idea what might be the issue here or how to solve it (in a
> consistent way).
>
> -Maarten
>
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