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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