t1-freesurfer running but no outputs

[Mathilde Bateson]

It seems the t1-freesurfer pipeline is running but not saving any outputs

"Storing result file without outputs"

here is the log error I get 

Clinica, version 0.8.4 and Python 3.11.10

I also attach the full pypeline.log if useful.

What's happening ?

THanks !

Best 
mathilde

[Mathilde Bateson]

More info as asked in another similar problem

• the version of the dependencies I am using ? 
  • not sure what is meant ?
• the command line I use (as in "clinica run dwi-pre... your/paths/...")

clinica run t1-freesurfer /mnt/custom-file-systems/efs/fs-09913c1f7db79b6fd/data/bids_data/ /mnt/custom-file-systems/efs/fs-09913c1f7db79b6fd/data/caps

• a screenshot of a typical input

not sure what is meant but : 

Cheers
Mathidle

[Nicolas Gensollen]

Hello Mathilde,

Looking at the logs you provided, you have a problem with your installation of Freesurfer:

```

Cmdline: recon-all -all -i /mnt/custom-file-systems/efs/fs-09913c1f7db79b6fd/data/bids_data/sub-ADNI002S0413/ses-M036/anat/sub-ADNI002S0413_ses-M036_T1w.nii.gz -qcache -subjid sub-ADNI002S0413_ses-M036 -sd /tmp/tmp99fx8r78/t1-freesurfer/ReconAll/sub-ADNI002S0413_ses-M036 Stdout: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /tmp/tmp99fx8r78/t1-freesurfer/ReconAll/sub-ADNI002S0413_ses-M036 Actual FREESURFER_HOME /mnt/custom-file-systems/efs/fs-09913c1f7db79b6fd/freesurfer Linux default 5.10.228-219.884.amzn2.x86_64 #1 SMP Wed Oct 23 17:17:00 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux ERROR: OS is missing bc (binary calculator) utility Stderr: Traceback: RuntimeError: subprocess exited with code 1.

```

That is, when running the recon-all command above, freesurfer is crashing because there seems to be a missing utility for some reason.

Could you try installing this utility to see whether it solves the problem or not ? You should be able to do: "sudo apt install bc".

Let us know how it goes.

Best,

Nicolas