I am trying to run 3dTrackID for probabilistic tractography
3dTrackID -mode PROB -dti_in /Users/dti-afni*.nii.gz -netrois /Users/ROIs_GMI.nii.gz -uncert /Users/dti-afni_dwuncert.nii.gz -alg_Thresh_FA 0.2 -alg_Thresh_Frac 0.1 -alg_Nseed_Vox 5 -alg_Nmonte 1000 -prefix network6
However, every time I run this code I get the following error:
** ERROR: Failed to load ‘-netrois’ options.
I’m not sure why I keep getting this message. I used the GMI output from 3dROIMaker and transformed it into diffusion weighted space.
Thanks for your time, looking forward to your response.
That is not the correct way to provide the “-dti_in …” input. What comes after the “-dti_in” option is not a list of files (which is what is currently being provided). It is just the prefix of the files created by tensor fitting.
For example, if your output from tensor fitting created a lot of files in the “/Users/” directory called:
dti-afni_MD.nii.gz, dti-afni_FA.nii.gz, dti-afni_V1.nii.gz, dti-afni_V2.nii.gz, dti-afni_V3.nii.gz, dti-afni_L1.nii.gz, …
Then you would enter the commoon part of their prefix to the option name, such as:
3dTrackID -dti_in /Users/dti-afni ....
with all the rest of your options.
Please see the EXAMPLES section at the bottom of the 3dTrackID help file for more cases of this.
Ah, thank you for pointing that out.
I corrected it, and now it now works