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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 >>