5ttgen [WARNING] ACPCdetect not installed;

1

Hi

When running 5ttgen with the hsvs option I get the warning that ACPDetect is not installed and therefore “cannot segment anterior commissure”

Could you link me to instructions to install ACPDetect for 5ttgen hsvs? It’s quite important for me to segment the anterior commissure.

Cheers
James

2

Hi James,

ACPCdetect is part of the Automatic Registration Toolbox, and as far as I know, NITRC is the only place to find it.

If anybody knows of any alternative methods available for either segmenting, or simply automatically locating, the anterior commissure, I’d love to hear it; but this is the only thing I could find.

Rob

3

Hi Rob

Thanks for this explanation. I downloaded and installed the Mac Automatic Registration Toolbox and got it working but it’s missing the ACPCdetect module and the author has not replied to a query. I’ll try the Linux version and see if it solves it, but otherwise there’s a problem here I don’t know how to resolve.

Cheers
James

4

There does appear to be a Mac OSX download for ACPCdetect on the NITRC link above. It doesn’t actually need ART to be installed; I just download that one toolbox myself.

5

Hi Rob
Thanks for this, yes–silly of me not to see that I downloaded and installed but something’s not right. Somehow I think I’ve managed to mess up my Path so things are no longer functioning properly. I’ve hunted on the web unsuccessfully for a solution.
Here’s what it looks like when I open a new terminal window:
Last login: Mon Nov 16 19:04:21 on console
-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer/7.1.1
FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/jameshartzell/freesurfer
MNI_DIR /Applications/freesurfer/7.1.1/mni
FSL_DIR /usr/local/fsl
/etc/zshrc:7: command not found: locale
/etc/zshrc_Apple_Terminal:104: command not found: mkdir
(eval):116: command not found: dirname
(eval):116: command not found: dirname
__add_sys_prefix_to_path:6: command not found: dirname
__add_sys_prefix_to_path:7: command not found: dirname
touch: /Users/jameshartzell/.zsh_sessions/0620B365-297D-4F1B-AA90-54F8D6B06A41.historynew: No such file or directory
(base) jameshartzell@Jamess-MacBook-Pro ~ %

Would you mind to have a look at the attached files and see if you can tell me where I’ve gone wrong?
I removed the initial . and made them pdfs so they will upload here.
bashrc.pdf (12.1 KB) zprofile.pysave.pdf (14.2 KB) zshrc.pdf (17.0 KB) bash_profile.pdf (12.6 KB)

Cheers
James

6

Hi James,

Having never touched a Mac, I’ve not been subjected to the transition from bash to zsh as the default shell interpreter, so am not of much use here. Hopefully someone else can have a look. But I’d suggest at least that .bashrc and .bash_profile are likely to be having no effect on zsh's configuration.

Cheers
Rob

7

Hi Rob
Found the problem. Just needed to add the acpcdetect path correctly in .zprofile
Running 5ttgen now and it saw and is using acpcdetect.
Will let you know how it comes out, and hopefully finally answer your question about 5ttgen anatomical segmentation!
Cheers
James

8

3 posts were split to a new topic: 5ttgen hsvs segmentation around fornix