You can see that the vox_units are Unknown in the fslhd output. This is the source of the problem in FS.

On 12/18/2020 10:53 AM, Jonathan Lynn wrote:

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Hello,

I've been using a software to process SWI data that includes an option to save the output as nifti files. When I attempt to use either the mri_info or mri_convert commands on these nifti files I receive the following error message:

niiRead(): unknown space units 7 in /pfc/common_area/high_pass_1750_1910.nii

Where "high_pass_1750_1910.nii" is the name of my nifti file. This leads me to believe there is a problem in how my SWI processing software saves nifti files which makes them incompatible with FreeSurfer. I am curious if it is a problem with some aspect of the nifti header information that is causing me to receive this error and if so, which aspect?

Using the fsl program fslhd I have gotten the header info for one of these nifti files and pasted it below:

filename high_pass_1750_1910.nii

sizeof_hdr 348 data_type INT16 dim0 4 dim1 232 dim2 256 dim3 176 dim4 1 dim5 0 dim6 0 dim7 0 vox_units Unknown time_units rad/s datatype 4 nbyper 2 bitpix 16 pixdim0 0.000000 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.000000 pixdim5 -nan pixdim6 6445431373862396660923732403945472.000000 pixdim7 6445014188069157487771091399081984.000000 vox_offset 352 cal_max 3253932511416847943508928692748288.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 6444907725225778945067450074398720.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code -99 slice_start 30622 slice_end -1814 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 73 ´õtent_name ëh`0 intent_p1 0.000000 intent_p2 6444907725225778945067450074398720.000000 intent_p3 68507965883187986432.000000 qform_name Unknown qform_code 0 qto_xyz:1 1.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 1.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 1.000000 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 aux_file ¤ô

I am hoping someone can help me understand why I am receiving this error from mri_info.

Thank you, John

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