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Subject:

Re: -applyxfm in flirt

From:

Rutvik Desai <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 23 Oct 2006 13:41:15 -0500

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (218 lines)

Thanks, after modifying the header as suggested it is working.
After applying the transform, I tried to change the registered
file back to original format (5 dimensions), but that does not
work (random data is displayed), but this is not a big problem
at all.

best,
Rutvik

On Oct 23, 2006, at 3:58 AM, Mark Jenkinson wrote:

> Hi,
>
> I'm afraid that your input image uses a more advanced feature of
> nifti that we are not currently supporting (vector and matrix
> data, where dim5 and/or dim6 are >1 but dim4=1).  All of our
> "vector" data is currently treated as if it were a time series, by
> setting dim4>1.
>
> Hence, to make this work with FSL you will need to change the
> value of dim4 to 322 and set dim5 to 1.  I believe that nifti_tool
> (which should be available in AFNI) will be able to do this.
>
> All the best,
>    Mark
>
>
>
> Desai, Rutvik wrote:
>
>> The input file is the output of the AFNI program 3dDeconvolve.
>> It was converted to nifti format with 3dAFNItoNIFTI command.
>> (3dAFNItoNIFTI was also used to convert the raw data to nifti,
>> for with -applyxfm works fine).
>>
>> Here is the output of avwhd for the input file and for the output
>> file:
>>
>> INPUT (statmap):
>>
>> filename       1225.RLSPDF.bucket.nii.gz
>>
>> sizeof_hdr     348
>> data_type      FLOAT32
>> dim0           5
>> dim1           64
>> dim2           64
>> dim3           36
>> dim4           1
>> dim5           322
>> dim6           1
>> dim7           1
>> vox_units      mm
>> time_units     Unknown
>> datatype       16
>> nbyper         4
>> bitpix         32
>> pixdim0        0.0000000000
>> pixdim1        3.2500000000
>> pixdim2        3.2500000000
>> pixdim3        3.2999999523
>> pixdim4        1.0000000000
>> pixdim5        1.0000000000
>> pixdim6        1.0000000000
>> pixdim7        1.0000000000
>> vox_offset     22144
>> 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      -3.250000  0.000000  0.000000  102.375000
>> qto_xyz:2      0.000000  -3.250000  0.000000  132.375000
>> qto_xyz:3      0.000000  0.000000  3.300000  -27.500000
>> 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      -3.250000  0.000000  0.000000  102.375000
>> sto_xyz:2      0.000000  -3.250000  0.000000  132.375000
>> sto_xyz:3      0.000000  0.000000  3.300000  -27.500000
>> 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        aux_file
>> OUTPUT:
>>
>> Darwin birdie rhdesai ~/pub/SenLit/sl.1225/AFNIWORK 207: avwhd  
>> 1225.RLSPDF.bucket.reg.nii.gz filename        
>> 1225.RLSPDF.bucket.reg.nii.gz
>>
>> sizeof_hdr     348
>> data_type      FLOAT32
>> dim0           3
>> dim1           256
>> dim2           256
>> dim3           134
>> dim4           1
>> dim5           1
>> dim6           1
>> dim7           1
>> vox_units      mm
>> time_units     s
>> datatype       16
>> nbyper         4
>> bitpix         32
>> pixdim0        0.0000000000
>> pixdim1        0.8125000000
>> pixdim2        0.8125000000
>> pixdim3        1.0000000000
>> pixdim4        1.0000000000
>> pixdim5        1.0000000000
>> pixdim6        1.0000000000
>> pixdim7        1.0000000000
>> vox_offset     22144
>> 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      -0.812500  0.000000  0.000000  103.593803
>> qto_xyz:2      0.000000  -0.812500  0.000000  133.593994
>> qto_xyz:3      0.000000  0.000000  1.000000  -40.000000
>> 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      -0.812500  0.000000  0.000000  103.593803
>> sto_xyz:2      0.000000  -0.812500  0.000000  133.593994
>> sto_xyz:3      0.000000  0.000000  1.000000  -40.000000
>> 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        FSL3.3
>> aux_file
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
>> Sent: Sun 10/22/2006 3:37 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] -applyxfm in flirt
>> Hi,
>>
>> This might be due to how the original image (statmap)
>> was formed.  Can you describe how you generated it?
>> Also, please send us the output of avwhd on the input
>> and output files.
>>
>> All the best,
>> 	Mark
>>
>>
>> On 22 Oct 2006, at 05:43, Rutvik Desai wrote:
>>
>>
>>> I am tring to apply a transformation matrix (calculated
>>> using flirt) to a statistical parametric map, but the output is
>>> not correct.
>>>
>>> flirt -in statmap.nii -init flirt.mat -applyxfm -ref anat.bet.nii  
>>> -out
>>> statmap.reg
>>>
>>> The statmap has many datapoints per voxel (t-stats, betas,  
>>> etc.),  but the
>>> resulting statmap.reg has only one datapoint (only one BRIK in
>>> AFNI jargon) for some reason.
>>>
>>> If the same command is run with the raw data as input instead of the
>>> statmap, the output is correct as expected with all the datapoints.
>>> Any ideas?
>>>
>>> Thanks,
>>> Rutvi
>>>
>> k
>>

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