fMRIprep error with ants

1

Dear experts,

I’m running fMRIprep for the first time with the following command:

singularity run -C -B /EBC:/EBC /EBC/home/mblesa/fmriprep-20.2.3.simg /EBC/home/mblesa/BIDS/fMRIprep_tentative /EBC/home/mblesa/BIDS/fMRIprep_tentative/OUTPUT_syn participant --participant-label sub-003 -w /EBC/home/mblesa/BIDS/ --fs-no-reconall --nthreads 16 --omp-nthreads 16 --fs-license-file /EBC/local/infantFS/freesurfer/license.txt --output-space MNI152NLin2009cAsym:res-2 --stop-on-first-crash > ../log.txt

There was an error in the registration with the template, that made the process crash (please see attached the log). Any clue on how to solve it? Thanks in advance.

Best regards,

Manuel

log.txt (308.0 KB)

2

Looks like templateflow cache is being made in the /root drive. Do you have permission to read/write there?

3

Hi,

I should have, but just in case, how I can change the cache location? Thanks in advance.

Best regards,

Manuel

4

you can change the environment variable TEMPLATFLOW_HOME Python Client - TemplateFlow

Also, try updating to the most recent fmriprep verision (20.2.5)

5

Hi @Steven,

I tried your suggestion adding:

export TEMPLATEFLOW_HOME=/EBC/home/mblesa/BIDS/fMRIprep_tentative

before launching fMRIprep, but it seems is ignoring this and still showing the same error. Maybe I have to define it in another way? Thanks in advance.

Best regards,

Manuel

6

Just to be sure, have you tried updating to most recent fmripre version?

7

Environment variables you want to pass inside singularity containers should be prefixed with SINGULARITYENV_. See Executing with Singularity - NiPreps.

8

Hi,

Thanks for your replies. I still get the same error. I updated to the latest version (20.2.5) and I’m adding the following command before:

export SINGULARITYENV_TEMPLATEFLOW_HOME=/EBC/home/mblesa/BIDS/fMRIprep_tentative

Any clue?

Best regards,

Manuel