R: R: [Camino-users] R: bg mask track error
Curci Marina Carmela
marina.curci at epfl.ch
Wed Jul 11 13:56:01 PDT 2012
But I'm producing one streamline per seed using a pds file..
________________________________________
Da: Philip A Cook [cookpa at mail.med.upenn.edu]
Inviato: mercoledì 11 luglio 2012 22.49
A: Curci Marina Carmela
Cc: camino-users at www.nitrc.org
Oggetto: Re: R: [Camino-users] R: bg mask track error
track counts seeds, procstreamlines counts streamlines, so the numbers will differ unless you are producing one streamline per seed.
On Jul 11, 2012, at 4:36 PM, Curci Marina Carmela wrote:
> 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
>> _______________________________________________
>> Camino-users mailing list
>> Camino-users at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/camino-users
>
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