[RESOLVED] Aborting execution in hcp_freesurfer

Use Questions
1

Hi,

I am trying to process amounts of data, but some of data failed at the step “hcp_freesurfer”.
Here is the error log:

Session id: FCS_194_A
[started on Thursday, 19. June 2025 08:33:26]

Running HCP FreeSurfer Pipeline [LegacyStyleData] ...

---> PreFS results present.

------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh
    --session-dir="/mnt/hdd1/yumingz/washingtonu/script/script/sessions/FCS_194_A/hcp/FCS_194_A/T1w"
    --session="FCS_194_A"
    --processing-mode="LegacyStyleData"
    --t1="/mnt/hdd1/yumingz/washingtonu/script/script/sessions/FCS_194_A/hcp/FCS_194_A/T1w/T1w_acpc_dc_restore.nii.gz"
    --t1brain="/mnt/hdd1/yumingz/washingtonu/script/script/sessions/FCS_194_A/hcp/FCS_194_A/T1w/T1w_acpc_dc_restore_brain.nii.gz"
    --t2="NONE"
------------------------------------------------------------

 ---> removing preexisting FS folder [/mnt/hdd1/yumingz/washingtonu/script/script/sessions/FCS_194_A/hcp/FCS_194_A/T1w/FCS_194_A]

Running HCP FS

ERROR: Running HCP FS failed with error 1

For better address this problem, the error log files are attached belowed:
error_hcp_freesurfer_FCS_194_A_2025-06-19_08.33.28.981208.log (159.0 KB)
recon-all.log (166.4 KB)

Many thanks for your kindly help!

Best,
Acacius

2

Hi,
did you use SLURM (or any other scheduler)? What settings did you use? Did you try to use more RAM?

3

Hi Acacius,

There is a keyword killed in your log. This happens when the system kills the QuNex process. Most common cuprits are running out of memory or disk and hitting the designated process walltime.

Best, Jure

4

Hi, Matkovic

Thanks for your kindly help. Yes, I am trying to allocate more RAM to run the program again, hoping that it will work.

Best,
Acacius

5

Hi, Jure

Thanks for your reply. I am trying to allocate more RAM to run the program again, hoping that this will work.

Best
Acacius