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: 5ttgen: [Errno 2] No such file or directory 5ttgen: 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