R: [Camino-users] R: bg mask track error
Curci Marina Carmela
marina.curci at epfl.ch
Wed Jul 11 13:36:22 PDT 2012
I refer to the number of seed points that I read when i run track and to the number that i see after I run procstreamlines
________________________________________
Da: Philip A Cook [cookpa at mail.med.upenn.edu]
Inviato: mercoledì 11 luglio 2012 22.32
A: Curci Marina Carmela
Oggetto: Re: [Camino-users] R: bg mask track error
Hi,
How are you counting the streamlines?
On Jul 11, 2012, at 3:14 PM, Curci Marina Carmela wrote:
> Hello....sorry for the spam...It's just to say that I solved my problem...
>
> I have a question: if I run the track command and then procstreamlines using as input for track the pds file, I have noticed that the number of streamlines generated with track is different from the number of streamlines processed by procstreamlines. Could you explain to me the reason, please??
>
> Thank you for your help!!!
> Marina
> ________________________________________
> Da: Curci Marina Carmela
> Inviato: mercoledì 11 luglio 2012 15.14
> A: camino-users at www.nitrc.org
> Oggetto: bg mask track error
>
> Hello to everyone!!
> I'm running DTI and deterministic tractography on 2 different datasets with 2 different resolutions.
> Because of the seedfile has different dimensions from input file I use the option -header and I use also the option -bgmask using as background mask the white matter mask.
> This method works well with one dataset, but not with the other one, because I receive the following error:
>
> 'Brain mask must be in the same voxel space as the input data'
>
> I suppose there is a sort of conflict between the bgmask and the dataset, but I don't understand the problem.
> I estimate the diffusion tensor using the bgmask but I don't have any kind of problem.
>
> Could you help me please??
>
> Maybe the headers could be useful for you:
>
> DATASET WITH ERROR
>
> DATASET (argument for option -header)
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 128
> dim2 128
> dim3 36
> dim4 65
> dim5 0
> dim6 0
> dim7 0
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 3.0000000000
> pixdim4 8.1000003815
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 0.000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -1.999997 -0.003654 0.000000 130.620819
> qto_xyz:2 0.003654 -1.999997 0.000000 138.607727
> qto_xyz:3 0.000000 0.000000 3.000000 -24.710392
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> 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 SIEMENS TrioTim 3T
>
>
> BGMASK
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 128
> dim2 128
> dim3 36
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 3.0000000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -1.999997 -0.003654 0.000000 130.620819
> qto_xyz:2 0.003654 -1.999997 0.000000 138.607758
> qto_xyz:3 0.000000 0.000000 3.000000 -24.710392
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -1.999997 -0.003654 0.000000 130.620819
> sto_xyz:2 0.003654 -1.999997 0.000000 138.607758
> sto_xyz:3 0.000000 0.000000 3.000000 -24.710392
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Anterior-to-Posterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.1
>
>
>
> DATASET WITHOUT ERROR
>
> DATASET(argument for option -header)
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 96
> dim2 96
> dim3 34
> dim4 21
> dim5 0
> dim6 0
> dim7 0
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 2.2083332539
> pixdim2 2.2083332539
> pixdim3 3.0000000000
> pixdim4 6.0000000000
> pixdim5 0.0000000000
> pixdim6 0.0000000000
> pixdim7 0.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 0.000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -2.208333 0.000000 0.000000 107.204773
> qto_xyz:2 0.000000 -2.208333 0.000000 118.048157
> qto_xyz:3 0.000000 0.000000 3.000000 -36.849396
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> 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 SIEMENS TrioTim 3T
>
> BGMASK
> sizeof_hdr 348
> data_type FLOAT32
> dim0 3
> dim1 96
> dim2 96
> dim3 34
> dim4 1
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 16
> nbyper 4
> bitpix 32
> pixdim0 0.0000000000
> pixdim1 2.2083332539
> pixdim2 2.2083332539
> pixdim3 3.0000000000
> 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 Scanner Anat
> qform_code 1
> qto_xyz:1 -2.208333 0.000000 0.000000 107.204773
> qto_xyz:2 0.000000 -2.208333 0.000000 118.048149
> qto_xyz:3 0.000000 0.000000 3.000000 -36.849396
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Anterior-to-Posterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -2.208333 0.000000 0.000000 107.204773
> sto_xyz:2 0.000000 -2.208333 0.000000 118.048149
> sto_xyz:3 0.000000 0.000000 3.000000 -36.849396
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Anterior-to-Posterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.1
>
> Thank you for your availability,
> Marina
> _______________________________________________
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> Camino-users at www.nitrc.org
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