Hi Shane,
As long as the anatomical labels, when viewed in FSLeyes or FSLView
are correct, having the voxel coordinate system out of alignment is
generally not an issue within FSL.
However, it can help some processing steps (most notably registration)
to force the voxel orientation of all of your images to be the same -
you can use fslreorient2std to do this.
If the anatomical labels are incorrect, this is a more serious problem
that must be manually corrected using fslorient.
Cheers,
Paul
On 16/04/2019, Shane Schofield
<[log in to unmask]> wrote:
> Hi Taylor,
> Thanks for the advice. I have tried fslhd and the difference lies in the
> "sform_yorient Anterior-to-Posterior". (full output below). The rest of the
> dataset shows Posterior-to-Anterior. How may I go about fixing this? Will I
> need to change the BVEC and re-run EDDY? Appreciate your help.
> Best Regards,Shane
>
> 1) subject oriented differentlyfilename data.nii.gzsize of header
> 348data_type FLOAT32dim0 4dim1 96dim2 96dim3 63dim4 64dim5 1dim6 1dim7
> 1vox_units mmtime_units sdatatype 16nbyper 4bitpix 32pixdim0 1.000000pixdim1
> 2.000000pixdim2 2.000000pixdim3 2.000000pixdim4 1.000000pixdim5
> 0.000000pixdim6 0.000000pixdim7 0.000000vox_offset 352cal_max
> 0.000000cal_min 0.000000scl_slope 1.000000scl_inter 0.000000phase_dim
> 0freq_dim 0slice_dim 0slice_name Unknownslice_code 0slice_start 0slice_end
> 0slice_duration 0.000000toffset 0.000000intent Unknownintent_code
> 0intent_nameintent_p1 0.000000intent_p2 0.000000intent_p3 0.000000qform_name
> Scanner Anatqform_code 1qto_xyz:1 -1.988978 0.139083 -0.156918
> 90.772514qto_xyz:2 -0.139513 -1.995128 -0.000000 77.401260qto_xyz:3
> -0.156536 0.010946 1.993835 -44.100826qto_xyz:4 0.000000 0.000000 0.000000
> 1.000000qform_xorient Right-to-Leftqform_yorient
> Anterior-to-Posteriorqform_zorient Inferior-to-Superiorsform_name Scanner
> Anatsform_code 1sto_xyz:1 -1.988978 0.139083 -0.156918 90.772514sto_xyz:2
> -0.139513 -1.995128 -0.000000 77.401260sto_xyz:3 -0.156536 0.010946 1.993835
> -44.100826sto_xyz:4 0.000000 0.000000 0.000000 1.000000sform_xorient
> Right-to-Leftsform_yorient Anterior-to-Posteriorsform_zorient
> Inferior-to-Superiorfile_type NIFTI-1+file_code 1descrip 5.0.10aux_file
> 2) correctly orientedfilename data.nii.gzsize of header 348data_type
> FLOAT32dim0 4dim1 96dim2 96dim3 63dim4 64dim5 1dim6 1dim7 1vox_units
> mmtime_units sdatatype 16nbyper 4bitpix 32pixdim0 -1.000000pixdim1
> 2.000000pixdim2 2.000000pixdim3 2.000000pixdim4 1.000000pixdim5
> 0.000000pixdim6 0.000000pixdim7 0.000000vox_offset 352cal_max
> 0.000000cal_min 0.000000scl_slope 1.000000scl_inter 0.000000phase_dim
> 0freq_dim 0slice_dim 0slice_name Unknownslice_code 0slice_start 0slice_end
> 0slice_duration 0.000000toffset 0.000000intent Unknownintent_code
> 0intent_nameintent_p1 0.000000intent_p2 0.000000intent_p3 0.000000qform_name
> Scanner Anatqform_code 1qto_xyz:1 -1.997977 -0.066280 -0.060792
> 104.428230qto_xyz:2 -0.051752 1.952913 -0.428314 -101.056908qto_xyz:3
> -0.073555 0.426307 1.952652 -72.568550qto_xyz:4 0.000000 0.000000 0.000000
> 1.000000qform_xorient Right-to-Leftqform_yorient
> Posterior-to-Anteriorqform_zorient Inferior-to-Superiorsform_name Scanner
> Anatsform_code 1sto_xyz:1 -1.997977 -0.066280 -0.060794 104.428230sto_xyz:2
> -0.051752 1.952913 -0.428314 -101.056908sto_xyz:3 -0.073557 0.426307
> 1.952652 -72.568550sto_xyz:4 0.000000 0.000000 0.000000
> 1.000000sform_xorient Right-to-Leftsform_yorient
> Posterior-to-Anteriorsform_zorient Inferior-to-Superiorfile_type
> NIFTI-1+file_code 1descrip 5.0.10aux_file
> s On Monday, April 15, 2019, 9:50:33 AM GMT+1, Taylor Hanayik
> <[log in to unmask]> wrote:
>
> Hi,
> It’s difficult to say why this has happened without more info. Have you
> tried viewing the inputs to tbss_preproc to make sure they are all oriented
> the same way? Perhaps you could run fslhd MyImage.nii.gz on the subject
> oriented incorrectly, and also run fslhd on an image that matches the rest
> of the dataset. Send the output of both commands if you still haven’t
> resolved the issue by visually inspecting all the inputs passed to tbss.
>
> Cheers,
>
> Taylor Hanayik
>
>
> Taylor Hanayik PhDAnalysis Research Software Engineer
> FMRIB, John Radcliffe Hospital
> University of Oxford
> [log in to unmask]
>
>
>
>
>
> On 13 Apr 2019, at 08:51, Shane Schofield
> <[log in to unmask]> wrote:
> Hi TBSS Experts
> After running tbss_1_preproc, I noticed one of the subjects were oriented
> different compared to the rest of the study (flipped along the L-R axis,
> seen on saggital view) . May I know why is this happening and is this a
> cause of concern?
> Thank you.
> Best wishes,Shane
>
>
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