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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