Hi there!
I am using single-shell data and following these steps in MRtrix documentation, which is, however, written for group analysis and I am having trouble adjusting the analysis.
In step 5 (global intensity normalization across subjects), I choose individual instead of group as an algorithm. After which I continue with dwi2response tournier, DWI unsampling, mask generation, but I run into problems is step 9 (Fibre Orientation Distribution estimation). I don’t fully understand what the recommended code does in using dwiextract and dwi2fod in one command:
for_each * : dwiextract IN/dwi_denoised_unringed_preproc_unbiased_normalised_upsampled.mif - \| dwi2fod msmt_csd - ../group_average_response.txt IN/wmfod.mif -mask IN/dwi_mask_upsampled.mif
So I simply run,
dwi2fod msmt_csd dwi_den_preproc_unbiased_norm_upsampled.mif response.txt wmfod.mif -mask dwi_mask_upsampled.mif
and I run into problems:
dwi2fod msmt_csd dwi_den_preproc_unbiased_norm_upsampled.mif response.txt wmfod.mif -mask dwi_mask_upsampled.mif -debug
dwi2fod: [DEBUG] No config file found at "/etc/mrtrix.conf"
dwi2fod: [DEBUG] No config file found at "/Users/dominika/.mrtrix.conf"
dwi2fod: [INFO] opening image "dwi_den_preproc_unbiased_norm_upsampled.mif"...
dwi2fod: [DEBUG] reading key/value file "dwi_den_preproc_unbiased_norm_upsampled.mif"...
dwi2fod: [DEBUG] sanitising image information...
dwi2fod: [INFO] image "dwi_den_preproc_unbiased_norm_upsampled.mif" opened with dimensions 184x184x102x40, voxel spacing 1.2 x1.25x1.25x4.5999999999999996, datatype Float32LE
dwi2fod: [INFO] opening image "dwi_mask_upsampled.mif"...
dwi2fod: [DEBUG] reading key/value file "dwi_mask_upsampled.mif"...
dwi2fod: [DEBUG] sanitising image information...
dwi2fod: [INFO] image "dwi_mask_upsampled.mif" opened with dimensions 184x184x102, voxel spacing 1.25x1.25x1.25, datatype Bit
dwi2fod: [DEBUG] memory-mapping file "dwi_mask_upsampled.mif"...
dwi2fod: [DEBUG] file "dwi_mask_upsampled.mif" mapped at 0x10b14d000, size 431664 (read-only)
dwi2fod: [DEBUG] image "dwi_mask_upsampled.mif" loaded
dwi2fod: [DEBUG] image "dwi_mask_upsampled.mif" initialised with strides = [ -1 184 33856 ], start = 183, using direct IO
dwi2fod: [DEBUG] searching for suitable gradient encoding...
dwi2fod: [DEBUG] b-value scaling: max scaling factor = exp(inf) = inf
dwi2fod: [INFO] b-values scaled by the square of DW gradient norm (maximum scaling factor = inf)
dwi2fod: [INFO] found 40x4 diffusion gradient table
dwi2fod: [INFO] Diffusion gradient encoding data clustered into 1 non-zero shells and 10 b=0 volumes
dwi2fod: [DEBUG] Shells: b = { 0(10) 1000.0000679357424(30) }
dwi2fod: [DEBUG] No DW shells to be removed
dwi2fod: [DEBUG] loading matrix file "response.txt"...
dwi2fod: [DEBUG] found 1x6 matrix in file "response.txt"
dwi2fod: [DEBUG] unmapping file "dwi_mask_upsampled.mif"
dwi2fod: [DEBUG] image "dwi_mask_upsampled.mif" unloaded
dwi2fod: **[ERROR] number of rows in response functions must match number of b-value shells; number of shells is 2, but file "response.txt" contains 1 rows**
Thank you for any help,
Dominika