Hi Rob,
Thanks a lot for the quick reply.
I re-ran the command with the -debug flag and this is the output:
mtnormalise -mask /data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz wm_fod.mif wm_fod_norm.mif gm_scalar.mif gm_scalar_norm.mif csf_scalar.mif csf_scalar_norm.mif -debug
mtnormalise: [DEBUG] No config file found at "/etc/mrtrix.conf"
mtnormalise: [DEBUG] No config file found at "/home/remoteuser/treste/.mrtrix.conf"
mtnormalise: [INFO] opening image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz"...
mtnormalise: [DEBUG] transforms_match: FOV difference in scanner coordinates: 0
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] Axes and transform of image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz" altered to approximate RAS coordinate system
mtnormalise: [DEBUG] searching for suitable phase encoding data...
mtnormalise: [INFO] image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz" opened with dimensions 145x174x145, voxel spacing 1.25x1.25x1.25, datatype Float32LE
mtnormalise: [DEBUG] loading image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz"...
mtnormalise: [100%] uncompressing image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz"
mtnormalise: [DEBUG] image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz" loaded
mtnormalise: [DEBUG] image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz" initialised with strides = [ -1 145 25230 ], start = 144, 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 = [ -1 145 25230 ], start = 144, using direct IO
mtnormalise: [INFO] mask image contains 767938 voxels
mtnormalise: [DEBUG] image "/data/neuralabc/treste/Mult_dim_quant_WM/source/108525/T1w/Diffusion/nodif_brain_mask.nii.gz" unloaded
mtnormalise: [INFO] opening image "wm_fod.mif"...
mtnormalise: [DEBUG] reading key/value file "wm_fod.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "wm_fod.mif" opened with dimensions 145x174x145x45, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "wm_fod.mif"...
mtnormalise: [DEBUG] file "wm_fod.mif" mapped at 0x7efc40f02000, size 658503000 (read-only)
mtnormalise: [DEBUG] image "wm_fod.mif" loaded
mtnormalise: [DEBUG] image "wm_fod.mif" initialised with strides = [ -45 6525 1135350 1 ], start = 6480, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 28 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "wm_fod.mif"
mtnormalise: [DEBUG] image "wm_fod.mif" unloaded
mtnormalise: [INFO] opening image "gm_scalar.mif"...
mtnormalise: [DEBUG] reading key/value file "gm_scalar.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "gm_scalar.mif" opened with dimensions 145x174x145x1, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "gm_scalar.mif"...
mtnormalise: [DEBUG] file "gm_scalar.mif" mapped at 0x7efc67508000, size 14633400 (read-only)
mtnormalise: [DEBUG] image "gm_scalar.mif" loaded
mtnormalise: [DEBUG] image "gm_scalar.mif" initialised with strides = [ -1 145 25230 145 ], start = 144, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 28 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "gm_scalar.mif"
mtnormalise: [DEBUG] image "gm_scalar.mif" unloaded
mtnormalise: [INFO] opening image "csf_scalar.mif"...
mtnormalise: [DEBUG] reading key/value file "csf_scalar.mif"...
mtnormalise: [DEBUG] sanitising image information...
mtnormalise: [INFO] image "csf_scalar.mif" opened with dimensions 145x174x145x1, voxel spacing 1.25x1.25x1.25x1, datatype Float32LE
mtnormalise: [DEBUG] memory-mapping file "csf_scalar.mif"...
mtnormalise: [DEBUG] file "csf_scalar.mif" mapped at 0x7efc67503000, size 14633400 (read-only)
mtnormalise: [DEBUG] image "csf_scalar.mif" loaded
mtnormalise: [DEBUG] image "csf_scalar.mif" initialised with strides = [ -1 145 25230 145 ], start = 144, using direct IO
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 28 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [DEBUG] unmapping file "csf_scalar.mif"
mtnormalise: [DEBUG] image "csf_scalar.mif" unloaded
mtnormalise: [INFO] initialising basis...
mtnormalise: [DEBUG] initialising threads...
mtnormalise: [DEBUG] launching 28 threads "loop threads"...
mtnormalise: [DEBUG] waiting for completion of threads "loop threads"...
mtnormalise: [DEBUG] threads "loop threads" completed OK
mtnormalise: [INFO] outlier rejection quartiles: [ -inf -inf ]
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