Hi all,
I am trying to work through the fixel-based analysis script of MRtrix when I ran into the following error. The population_template command does not work because of an apparent typo after -nthreads 0 and linear_transforms etc. (see picture). Google and chat GPT advice me to alter the script of population_template but I don’t know how to. Or could the typo origin from my own script of population_template?
Thanks in advance!
Best, Jesca
To add some information:
Since the error states that there are 3 arguments required and we only supply 2, this may be because of the extra 0 that is added to linear_transformations_0/p1612.txt. It think that comes from the -nthreads function in the original code of MRtrix.
I have already tried to add a space where mrtrix says that it misses an argument at the original code from MRtrix. That didn’t solve it yet…
Hi Jesca,
Could you maybe post the exact command you try to run?
Also, did you check the completeness of the input?.. e.g., subject normalized wm fod and mask pairs
Cheers
William
below is the command, I ran (Note, I also declared some of the defaults, which is not necessary of course. I just added them to have them explicitly in the script)
population_template ${FOD_DIR} ${TEMPLATE_DIR}/wmfod_template.mif \
-type rigid_affine_nonlinear \
-voxel_size 1 \
-initial_alignment robust_mass \
-mask_dir ${MASK_DIR} \
-warp_dir ${WARP_DIR} \
-linear_transformations_dir ${LINEAR_TRANSFORM_DIR} \
-template_mask ${TEMPLATE_DIR}/wmfod_template_mask.mif \
-transformed_dir ${TRANSFORMED_DIR} \
-aggregate mean \
-scratch ${SCRATCH_DIR} \
-info \
-force
