Hi Mark,
Thanks for your reply. However, it doesn't seem to work. The resulting image is only a part of the brain (see enclosed screenshot).
Any ideas how I can solve this?
Thanks
Heidi
________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Mark Jenkinson [[log in to unmask]]
Verzonden: woensdag 5 juni 2013 23:41
Aan: [log in to unmask]
Onderwerp: Re: [FSL] visualizing results
Hi,
This is not a well-formed image as the number of voxels are consistent with a 3mm image (dim1-dim3 in the range 60-72) but the voxel sizes are wrong (pixdim1-pixdim3=1.0). The easiest way to resample images onto the melodic standard-space output is to do:
flirt -in $FSLDIR/data/standard/MNI152_T1_1mm -ref existing_melodic_image_3mm -usesqform -applyxfm -out mni_3mm
This uses an existing melodic result (existing_melodic_image_3mm) that is already in the 3mm standard space, and then resamples the standard MNI image to make sure that the mm coordinates align (this is what the -usesqform option does). Other commands can also achieve the same result, but sometimes it can be more difficult because it might be off 1 in the number of voxels (e.g. 61 vs 60) and this is a problem for FSLView.
All the best,
Mark
On 4 Jun 2013, at 21:58, Jacobs H (NP) <[log in to unmask]> wrote:
> Hi FSL developers,
>
> I wanted to check my results from my resting state analyses in fslview.
> In melodic I chose a resampling resolution of 3mm.
> So, I thought I would need to check my dual regression on a 3mm isotropic standard brain of FSL? Therefore, I used mri_convert to resample it in 3mm.
> However, my results do not fit on the standard MNI152_T1 1mm/2mm/3mm?
> I checked my output file with fslhd and I copied the result below this email.
> I was able to check the results on the bg_image.nii.gz. So, that was not a problem, but the atlas did not work properly (stating that the parietal lobe is the frontal lobe)?
>
> Any help?
>
> Thanks
> Heidi
>
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 60
> dim2 72
> dim3 60
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> time_offset 0.000000
> intent Unknown
> intent_code 0
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Unknown
> qform_code 0
> qto_xyz:1 1.000000 0.000000 0.000000 0.000000
> qto_xyz:2 0.000000 1.000000 0.000000 0.000000
> qto_xyz:3 0.000000 0.000000 1.000000 0.000000
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Left-to-Right
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Unknown
> sform_code 0
> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
> sto_xyz:4 0.000000 0.000000 0.000000 0.000000
> sform_xorient Unknown
> sform_yorient Unknown
> sform_zorient Unknown
> file_type NIFTI-1+
> file_code 1
> descrip FSL5.0
> aux_file
>
>
>
> ================================================
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> [log in to unmask]
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> ================================================
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