Dear MRtrix3 users,
I’m still familiarizing myself with MRtrix3, so I apologize for such a newbie question.
I’ve been following the Fibre Density Cross-section tutorial, but got stuck on item 5 as I keep getting the error message below:
INCEs-Mac-Pro:Teste_MRITRIX_group INCE$ cd dwiintensitynorm/
INCEs-Mac-Pro:dwiintensitynorm INCE$ ls
dwi_input dwi_output mask_input
INCEs-Mac-Pro:dwiintensitynorm INCE$ dwiintensitynorm dwi_input/ mask_input/ dwi_output/ fa_template.mif fa_template_wm_mask.mif -force
dwiintensitynorm: performing global intensity normalisation on 4 input images Traceback (most recent call last): File “/Users/INCE/mrtrix3/bin/dwiintensitynorm”, line 70, in prefix = i.split(commonPostfix)[0] ValueError: empty separator
INCEs-Mac-Pro:dwiintensitynorm INCE$
Any ideas? I’d really appreciate any help!
Cheers,
Joselisa
Thank you for your suggestion, but everything is looking good (no hidden files whatsoever):
INCEs-Mac-Pro:dwiintensitynorm INCE$ ls -a
. … dwi_input dwi_output mask_input
INCEs-Mac-Pro:dwiintensitynorm INCE$ cd dwi_input/
INCEs-Mac-Pro:dwi_input INCE$ ls -a
. C01574_dwi_denoised_preproc_bias.mif P00665_dwi_denoised_preproc_bias.mif
… C01575_dwi_denoised_preproc_bias.mif P00676_dwi_denoised_preproc_bias.mif
INCEs-Mac-Pro:dwi_input INCE$ cd …
INCEs-Mac-Pro:dwiintensitynorm INCE$ cd dwi_output/
INCEs-Mac-Pro:dwi_output INCE$ ls -a
. …
INCEs-Mac-Pro:dwi_output INCE$ cd …
INCEs-Mac-Pro:dwiintensitynorm INCE$ cd mask_input/
INCEs-Mac-Pro:mask_input INCE$ ls -a
. C01574_dwi_denoised_preproc_bias_mask.mif P00665_dwi_denoised_preproc_bias_mask.mif
… C01575_dwi_denoised_preproc_bias_mask.mif P00676_dwi_denoised_preproc_bias_mask.mif
It worked! I feel kinda dumb…I think the problem was a space at the end of some of the filenames that I couldn’t see without the tree function you suggested.
Thank you very much for your help!
Cheers from Brazil,
Joselisa
ln: illegal option – r
usage: ln [-Ffhinsv] source_file [target_file]
ln [-Ffhinsv] source_file … target_dir
link source_file target_file
However, just copying the files works (without the"-sr").
It also seems, that the option -sr is not known, just -s (that produced Alias-files, which ended up in not working for dwiintensitynorm and seemed to be understood as folders at first, but I’m not sure if that was because of DS_Store files which might have been produced by that process).
After copying, I received .DS_Store files. So installing “tree” via
brew install tree
revealed those files. After that I was able to proceed with step 5.