Lauren

It's unfortunately a P.I. requirement, which really is a pain because all my other ANTs scripts are in BASH, as you said, and at least using BASH fewer stupid questions come up.

I think I solved my own problem. It's definitely not an ANTs thing, it's a tcsh thing. I just put set nonomatch above that command and it seems like it's working now. You can tell I'm not a computer person. I hate tcsh and don't get this behavior at all but I think this fixes the issue?

Hey guys I'm really sorry but have one more issue I've run into. After changing up my .bash_profile as directed I have found that all my new ANTs scripts work as expected. However I tried to inset a command to antsAI in a tcsh script and am getting an error. I have removed the following command from the script: antsAI -c [10,0.000001,10] -d 3 -x /Volumes/DISS/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/Volumes/DISS/templateflow/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,vr_base.nii,32,Regular,0.200000]...

Awesome, I'll go this route then. Incidentially this was my first thought but was not entirely sure what having a path that includes (in it's whole hierarchy) multiple copies of certain commands ( say antsRegistration) would do to that particular command. Thanks for the help, and for the explanation. It's very useful just for learning in general how repositories work.

Oh jeezy ok, so I thought I had done this correctly but I'm not exactly sure WHAT happened but I apparently created a folder called /Applications/ANTs/bin/bin although I swear to God I c-maked to the correct directory. The new functions are in this /bin/bin directory instead of one up so when I try to run, say antsAI from any other folder I get the whole "command not found" error. So I just copied antsAI to the regular /Applications/ANTs/bin/ folder and this fixes the problem. So is it kosher for...

You know, I thought I had was smart enough to clone the repo where the binaries were but couldn't remember because I did it a year ago and couldn't really envision a scenario where I did NOT do that but, that's exactly what happened. Sorry for the dumbass question Nick, I really appreciate your help because for some reason this just wasn't occurring to me. Updated. Appreciate it.

Hey guys: This might be an easy one because I feel in my bones I'm just missing something obvious but: I need to update ANTs. Typing which ants gives me: /Applications/ANTs/bin/ants cd-ing into /Applications/ANTs and typing git pull origin master gives the error: fatal: Not a git repository (or any of the parent directories): .git This happens for the /bin/ folder as well as all other folders in this hierarchy. I have a lot of programs 'linked' to ANTs so didn't want to do a complete reinstall for...

Hi Dominik: I'm running a DCM on my fear conditioning study and wanted to double check something. I've got 3 CSs - a CS+ that is always followed by a shock 12s later, a CS- which is never followed by a shock, and a CST which is always followed by a shock but either 6, 8 ,10, or 12s later. My ISIs are also variable - 4, 6, 8 or 10s. When setting up my model I followed the DCM tutorial in that I made a timing file consisting of the onset & offset of all the CSs where the offset was when the shock occurred...