Tcksift2: Processing mask is empty

Dear experts,

I am running some data with sift2 (debug dump below). I am getting an error in two subjects “tcksift2: Processing mask is empty” … though I really cannot tell what the issue is. All the input images look fine to me. The registration seems to have been good between all the modalities, I cannot see what the problem could be.

Anyone encountered this before?

Claude

tcksift2 -act /media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif /media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_10M_prob.tck /media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif /media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_10M_prob.sift -debug -output_debug
tcksift2: [DEBUG] No config file found at "/etc/mrtrix.conf"
tcksift2: [DEBUG] No config file found at "/home/cbajada/.mrtrix.conf"
tcksift2: [INFO] opening image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif"...
tcksift2: [DEBUG] reading key/value file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif"...
tcksift2: [DEBUG] sanitising image information...
tcksift2: [INFO] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif" opened with dimensions 100x100x84x45, voxel spacing 2x2x2xnan, datatype Float32LE
tcksift2: [DEBUG] memory-mapping file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif"...
tcksift2: [DEBUG] file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif" mapped at 0x7f2ad3f79000, size 151200000 (read-only)
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif" loaded
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif" initialised with strides = [ -45 4500 450000 1 ], start = 4455, using direct IO
tcksift2: [DEBUG] sanitising image information...
tcksift2: [DEBUG] allocating scratch buffer for image "fixel map voxels"...
tcksift2: [DEBUG] image "fixel map voxels" loaded
tcksift2: [DEBUG] image "fixel map voxels" initialised with strides = [ -1 100 10000 ], start = 99, using direct IO
tcksift2: [DEBUG] sanitising image information...
tcksift2: [DEBUG] allocating scratch buffer for image "SIFT model processing mask"...
tcksift2: [DEBUG] image "SIFT model processing mask" loaded
tcksift2: [DEBUG] image "SIFT model processing mask" initialised with strides = [ -1 100 10000 ], start = 99, using direct IO
tcksift2: [INFO] opening image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif"...
tcksift2: [DEBUG] reading key/value file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif"...
tcksift2: [DEBUG] sanitising image information...
tcksift2: [INFO] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif" opened with dimensions 144x191x140x5, voxel spacing 1x1x1xnan, datatype Float32LE
tcksift2: [DEBUG] memory-mapping file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif"...
tcksift2: [DEBUG] file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif" mapped at 0x7f2acec68000, size 77011200 (read-only)
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif" loaded
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif" initialised with strides = [ -1 100800 -720 144 ], start = 100223, using direct IO
tcksift2: [DEBUG] sanitising image information...
tcksift2: [DEBUG] allocating scratch buffer for image "5TT scratch buffer"...
tcksift2: [DEBUG] image "5TT scratch buffer" loaded
tcksift2: [DEBUG] image "5TT scratch buffer" initialised with strides = [ -5 500 50000 1 ], start = 495, using direct IO
tcksift2: [DEBUG] initialising threads...
tcksift2: [DEBUG] launching 24 threads "loop threads"...
tcksift2: [100%] resampling ACT 5TT image to fixel image space...
tcksift2: [DEBUG] waiting for completion of threads "loop threads"...
tcksift2: [DEBUG] threads "loop threads" completed OK
tcksift2: [100%] resampling ACT 5TT image to fixel image space
tcksift2: [DEBUG] unmapping file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif"
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_5tt.mif" unloaded
tcksift2: [DEBUG] deleting scratch buffer for image "SIFT model processing mask"...
tcksift2: [DEBUG] image "SIFT model processing mask" unloaded
tcksift2: [DEBUG] deleting scratch buffer for image "5TT scratch buffer"...
tcksift2: [DEBUG] image "5TT scratch buffer" unloaded
tcksift2: [DEBUG] deleting scratch buffer for image "fixel map voxels"...
tcksift2: [DEBUG] image "fixel map voxels" unloaded
tcksift2: [DEBUG] unmapping file "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif"
tcksift2: [DEBUG] image "/media/cbajada/BSC-Data-02/Denmark_Data/sandbox/sub-0196/sub-0196_run-01_WM_FOD_norm.mif" unloaded
tcksift2: [ERROR] Processing mask is empty; check input images / registration

Hi Claude,

Can’t really offer much over and above the error message. Figured the most likely way to encounter such a case would be if there’s literally no overlap between the two images. But maybe you’ve found some creative way to get there. The process of resampling the 5TT image onto the DWI voxel grid is non-standard, so there’s some scope for that going wrong in some way, but I would think it would necessitate the 5TT image being malformed in some way; if you download / compile / run this command, its output may provide some clue. Beyond that, best bet is to share some data with me.

Cheers
Rob