`mtnormalize` NaN error

Kore_ana · November 28, 2022, 5:45pm

I got nan error when doing mtnormalize. I used -debug option to figure out what went wrong. Could anyone please tell me how I can solve this?

(base) MacBook-Pro-2:solve_mtnoramlize eunmi$ mtnormalise ./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif sub-160666_space-T1w_desc-preproc_dwi_wm_mtnorm.mif ./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif sub-160666_space-T1w_desc-preproc_dwi_gm_mtnorm.mif ./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif sub-160666_space-T1w_desc-preproc_dwi_csf_mtnorm.mif -check_mask inliers.nii.gz -mask ./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz -check_norm norm.nii.gz -nthreads 14 -debug
mtnormalise: [DEBUG] No config file found at "/etc/mrtrix.conf"
mtnormalise: [DEBUG] No config file found at "/Users/eunmi/.mrtrix.conf"
mtnormalise: [INFO] opening image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz"...
mtnormalise: [DEBUG] transforms_match: FOV difference in scanner coordinates: 0
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] Axes and transform of image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz" altered to approximate RAS coordinate system
mtnormalise: [DEBUG] searching for suitable phase encoding data...
mtnormalise: [INFO] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz" opened with dimensions 162x193x164, voxel spacing 1.2000000476837158x1.2000000476837158x1.2000000476837158, datatype Float32LE
mtnormalise: [DEBUG] loading image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz"...
mtnormalise: [100%] uncompressing image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz"
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz" loaded
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz" initialised with strides = [ -1 -162 31266 ], start = 31265, using indirect IO
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [DEBUG] allocating scratch buffer for image "index"...
mtnormalise: [DEBUG] image "index" loaded
mtnormalise: [DEBUG] image "index" initialised with strides = [ -1 -162 31266 ], start = 31265, using direct IO
mtnormalise: [INFO] mask image contains 392086 voxels
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/qsirecon_anat_wf/resample_mask/sub-160666_desc-brain_mask_resample.nii.gz" unloaded
mtnormalise: [INFO] opening image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif"...
mtnormalise: [DEBUG] reading key/value file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif" opened with dimensions 162x193x164x45, voxel spacing 1.2x1.2x1.2x0, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif"...
mtnormalise: [DEBUG] file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif" mapped at 0x109317000, size 922972320 (read-only)
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif" loaded
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif" initialised with strides = [ -45 -7290 1406970 1 ], start = 1406925, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 14 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif"
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_wm.mif" unloaded
mtnormalise: [INFO] opening image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif"...
mtnormalise: [DEBUG] reading key/value file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif" opened with dimensions 162x193x164x45, voxel spacing 1.2x1.2x1.2x0, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif"...
mtnormalise: [DEBUG] file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif" mapped at 0x109317000, size 922972320 (read-only)
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif" loaded
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif" initialised with strides = [ -45 -7290 1406970 1 ], start = 1406925, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 14 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif"
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_gm.mif" unloaded
mtnormalise: [INFO] opening image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif"...
mtnormalise: [DEBUG] reading key/value file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif" opened with dimensions 162x193x164x45, voxel spacing 1.2x1.2x1.2x0, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif"...
mtnormalise: [DEBUG] file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif" mapped at 0x109317000, size 922972320 (read-only)
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif" loaded
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif" initialised with strides = [ -45 -7290 1406970 1 ], start = 1406925, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 14 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif"
mtnormalise: [DEBUG] image "./sub-160666_mrtrix_multishell_msmt_hsvs/sub_160666_space_T1w_desc_preproc_recon_wf/msmt_csd/estimate_fod/sub-160666_space-T1w_desc-preproc_dwi_csf.mif" unloaded
mtnormalise: [INFO] initialising basis...
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 14 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [INFO]   outlier rejection quartiles: [ -1.4154708805422054 -1.2310470826045279 ]
mtnormalise: [INFO] Iteration: 1
mtnormalise: [DEBUG] Balance and outlier rejection iteration 1 starts.
mtnormalise: [100%] performing log-domain intensity normalisation
mtnormalise: [DEBUG] deleting scratch buffer for image "index"...
mtnormalise: [DEBUG] image "index" unloaded
mtnormalise: [ERROR] Non-positive tissue balance factor was computed. Balance factors: nan nan nan

Kore_ana · November 29, 2022, 11:49am

the mask used was :

Kore_ana · November 29, 2022, 11:49am

dwi_mf.mif was :

Kore_ana · November 29, 2022, 11:49am

dwi_csf.mif was :

Kore_ana · November 29, 2022, 11:49am

for additional information, the

dwi_gm.mif was :

mblesac · November 29, 2022, 6:51pm

Hi,

The mask looks strange, it includes the background right? I would say that is the problem, try using a mask that includes only the brain. I hope this helps.

Best regards,

Manuel

Kore_ana · December 3, 2022, 7:48am

Thank you for the response! You mentioned that masks might be wrong, but because this was made using QSIPREP, I am not 100% sure which mask I should be improving. I don’t know the details of how QSIPREP works, but I do know that I put in freesurfer results into the qsiprep as input. Could the T1w masks that are generated using freesurfer be the faulty ones?

mblesac · December 4, 2022, 10:26am

Hi,

I’m not sure about that. What you can do is to run dwi2mask in your diffusion data, then use that mask for the mtnormalise step.

Best regards,

Manuel