Hi, To elaborate my problem a little more ... Running FSL command avwhd gave me :
filename spiral.nii.gz sizeof_hdr 348 data_type INT16 dim0 4 dim1 64 dim2 64 dim3 25 dim4 250 dim5 1 dim6 1 dim7 1 vox_units Unknown time_units Unknown datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 3.7500000000 pixdim2 3.7500000000 pixdim3 4.0000000000 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 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 Unknown qform_code 0 qto_xyz:1 3.750000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 3.750000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 4.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior 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 FSL3.3 aux_file And avwhd on the spgr gave me: filename spgr.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 124 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 0.9375000000 pixdim2 0.9375000000 pixdim3 1.2000000477 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 7638.0000 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 -0.937500 0.000000 -0.000000 131.000000 qto_xyz:2 0.000000 0.937500 -0.000000 -119.197502 qto_xyz:3 0.000000 0.000000 1.200000 -77.393600 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 -0.937500 0.000000 0.000000 131.000000 sto_xyz:2 0.000000 0.937500 0.000000 -119.197502 sto_xyz:3 0.000000 0.000000 1.200000 -77.393600 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip FSL3.3 aux_file When I analyze the data in FSL I get the expected activation (Left hemisphere activation for right hand movement)so I know that FSL is reading or assuming the orientation correctly for the functional(even though sform and qform are unknown). My question is : after I run the recon-all process on the spgr, what do I need to do to the functional data to get freesurfer to read it correctly inorder to get proper output from reg-feat2anat? Any help is appreciated. Thanks Regards, Vish _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
