Hi all,
I’m new to MRtrix, so I hope my issue can be addressed easily (due to my misunderstanding). I ran into the following issue:
I have MRtrix FOD data, as generated by qsiprep. I segmented the FOD to fixels with:
$ fod2fixel sub-003_ses-mri01_acq-diffusion1p6mm16b0120b1250120b2500mb3x2_space-ACPC_model-msmtcsd_param-fod_label-WM_dwimap.mif.gz fixels -nii -maxnum 2
fod2fixel: \[100%\] uncompressing image “sub-003_ses-mri01_acq-diffusion1p6mm16b0120b1250120b2500mb3x2_space-ACPC_model-msmtcsd_param-fod_label-WM_dwimap.mif.gz”
fod2fixel: \[100%\] segmenting FODs
I then converted the output to (sparse) volumetric nifti format with (the NIFTI error is just FYI, all outcomes are the same if I use mif format):
$ fixel2voxel fixels/directions.nii none directions_2.nii
fixel2voxel: \[ERROR\] image “fixels/directions.nii” is not in NIFTI-1.1 format (sizeof_hdr != 348)
fixel2voxel: \[100%\] determining largest fixel count
fixel2voxel: \[100%\] converting sparse fixel data to scalar image
If I look at the dimensionality of the fixel direction-image I get the expected dim2 = 3
$ fslinfo fixels/directions.nii
data_type FLOAT32
dim1 472584
dim2 3
dim3 1
dim4 1
However, for the same data converted to volume, I get an unexpected dim4 = 2 (I expected it to be 6, i.e. 3 coordinate-values for fixel 1 and another 3 for fixel 2). How should I interpret this?
mentat001/dwi\_$ fslinfo directions_2.nii
data_type FLOAT32
dim1 101
dim2 123
dim3 107
dim4 2
(If I leave out -maxnum 2 in fod2fixel then I get dim4 = 11, which is just as weird)