5ttgen step acpcdetect failure on HPC

Hi all,

I am getting a 5ttgen error only when I submit my script as a job to a HPC using qsub. Not sure if I need to set a scratch folder to a particular directory manually in the HPC case, but getting the following error when T1RAS_16b.nii is referenced for acpcdetect. When I look in the scratch folder the nii file is there, and when I run the command normally, there doesn’t seem to be an issue. Any help would be greatly appreciated!

After running in job queue:

5ttgen: Running FSL FIRST to segment sub-cortical grey matter structures
Command:  run_first_all -s R_Thal,L_Puta,R_Caud,L_Amyg,R_Pall,R_Amyg,L_Caud,L_Hipp,R_Hipp,L_Thal,L_Pall,R_Accu,L_Accu,R_Puta -i T1.nii -b -o first
5ttgen: Mapping FIRST segmentations to image... [====================================================]
5ttgen: Using ACPCdetect and FAST to segment anterior commissure... [==========
5ttgen: [ERROR] acpcdetect -i T1RAS_16b.nii (hsvs.py:543)
5ttgen: [ERROR] Information from failed command:
        [Errno 2] No such file or directory
5ttgen: [ERROR] For debugging, inspect contents of scratch directory: /mnt/mfs/cndgrid/home/ch3658/5ttgen-tmp-MK9SSO/

Ran as normal:

5ttgen: FSL FIRST job may have been run via SGE; awaiting completion
5ttgen: (note however that FIRST may fail silently, and hence this script may hang indefinitely)
5ttgen: [  0%] Waiting for creation of 14 new items... 
5ttgen: [100%] Waiting for creation of 14 new items
5ttgen: [100%] Mapping FIRST segmentations to image
5ttgen: [100%] Using ACPCdetect and FAST to segment anterior commissure
5ttgen: [100%] Combining segmentations of all structures corresponding to each tissue type
5ttgen: [100%] Modulating segmentation images based on other tissues
5ttgen: Preparing images of cerebellum for intensity-based segmentation


Hi Caleb,

Can you please provide more information, including the exact command you are using, and also if you have loaded other modules in your HPC including FreeSurfer?


Hi Amir,

Thanks for your response. I am hitting that error while running a shell script with the following command set up:
5ttgen hsvs ${fsclean} ${mrtrix_dir}/5tt_t1space.mif

Can confirm using HPC for other modules such as FSL and FreeSurfer.

Let me know if I can provide further detail.