Hi,
I'm not sure what these messages exactly mean, but I would not necessarily assume that they were a problem since they appear to be a "note" rather than an "error". What happens if you use the bvecs in dtifit and look at the reconstructed directions, to see if they are anatomically correct? If these look OK then I would assume that the conversion is fine.
All the best,
Mark
On 25 Aug 2014, at 01:27, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I am converting my images from DICOM to NIFTI using dcm2nii.
>
> When doing the conversion, I am getting the following message (see below) and I am unsure if this could be a problem with the conversion.
>
> I would be very grateful if anyone of you could kindly guide me with this.
>
> Kind regards,
> Rosalia.
>
> Validating 31 potential DICOM images.
> Found 31 DICOM images.
> Converting 31/31 volumes: 31
> DTI2_1.MR.0005.0001.2011.05.22.19.01.19.203125.162996428.IMA->20110522_134235s005a001.nii
> 122
> Effective echo spacing: 0.3550054431ms, BandwidthPerPixelPhaseEncode: 23.0890007
> brightest voxel was 3380: data will be saved as 16-bit signed integer.
> GZip...20110522_134235s005a001.nii.gz
> Number of diffusion directions = 31
> Note: detected Siemens Software version [0018:1020] = 17
> -Will use 0019:000E or 0019:100E instead of 0029:1020 if version >= 15
> -Will stack across Acquisitions if version >=15
> -No slice angulation correction of vectors if version >=1000
> To adjust, edit /home/rosalia/.dcm2niigui/dcm2niigui.ini
> bvecs_old =[-0.2034116834,-0.5198867917,-0.8296635151]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.1970728785,-0.5202026963,-0.8309941292]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.4016382992,-0.176339671,-0.8986606598]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.4034495056,-0.7316343784,-0.5494903922]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.2017519772,-0.9418229461,-0.268822968]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.8529855609,-0.5187317133,-0.0577332303]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.7312694192,-0.5200868845,-0.4413101077]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.4072274864,-0.1768143624,-0.8960481882]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.732611537,-0.176131919,-0.6574631929]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.6500964165,-0.730713129,0.2084061801]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.3223554492,-0.9409121275,0.1037853435]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.3244359195,-0.5196797848,0.7903633714]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.6499877572,-0.5198718905,0.5543007255]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.9785525203,-0.1767190248,0.1058556736]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[-0.8546765447,-0.1767811179,0.4881357551]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.00073581,-0.7315701842,0.6817657351]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.00188608,-0.9418533444,0.3360187709]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.6540765166,-0.5197739005,0.5495623946]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.3291125596,-0.5199475288,0.7882509828]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.1977403015,0.1757074893,-0.9643783569]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.2040639669,-0.175633058,0.9630736113]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.6509756446,-0.7306162715,0.205986917]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.3236789703,-0.9411014318,0.0977741927]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.199726969,-0.9409098029,-0.273491621]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.4034495056,-0.7316343784,-0.5494903922]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.7322909832,-0.1760546267,-0.657841146]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.7286179066,-0.5195067525,-0.4463504553]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.8524485826,-0.5189238787,-0.0636347383]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.857454896,-0.1761782765,0.4834585786]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> bvecs_old =[0.9792180061,-0.176673457,0.099591203]';slice_dir =[0,0,1]';read_dir =[1,0,0]';phase_dir =[0,1,0]';
> Conversion completed in 21294 ms
>
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