fMRIPrep 25.0.0 and autorecon-2 and 3

,
1

I noticed that after running freesurfer through fMRIPrep, my pial surfaces have 0kb size and I read that fMRIPrep latest does not do autorecon-2 and 3 by default anymore. Is this true? If yes, does it mean we would have to do these two outside fMRIprep?

2

Hi @Divesh_Thaploo and welcome to neurostars!

In the future please use the software support post category and post template to provide us with information to help us help you.

I am not sure where you read that. fMRIPrep 25.0.0 Does do autorecon 2 and 3 as part of freesurfer.

Best,
Steven

3

Hi @Steven. Sure, I would do that. I am using the following script to run fMRIprep:

#!/bin/bash

# User inputs:
bids_root_dir="/mnt/c/Users/thaplood2/Documents/pre-post"
subj=04
nthreads=4
mem=12 #gb
container=docker #docker or singularity

# Begin:

# Convert virtual memory from gb to mb
mem=`echo "${mem//[!0-9]/}"` # remove gb at end
mem_mb=`echo $(((mem*1000)-5000))` # reduce some memory for buffer space during pre-processing

# export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
export FS_LICENSE="/mnt/c/Users/thaplood2/Documents/pre-post/derivatives/license.txt"

# Run fmriprep with Docker
if [ "$container" == "docker" ]; then
  unset PYTHONPATH; 
 docker run --rm -v $bids_root_dir:/data:ro -v $bids_root_dir/derivatives:/out:rw \
  -v $HOME/.cache/templateflow:/opt/templateflow:ro \
  -v /mnt/c/Users/thaplood2/Documents/pre-post/derivatives:/mnt/c/Users/thaplood2/Documents/pre-post/derivatives \
  -e FS_LICENSE=/mnt/c/Users/thaplood2/Documents/pre-post/derivatives/license.txt \
  nipreps/fmriprep:latest \
  /data /out participant \
  --participant-label $subj \
  --skip-bids-validation \
  --md-only-boilerplate \
  --fs-license-file /mnt/c/Users/thaplood2/Documents/pre-post/derivatives/license.txt \
  --output-spaces MNI152NLin2009cAsym:res-2 fsaverage fsnative \
  --nthreads $nthreads \
  --stop-on-first-crash \
  --mem $mem_mb

else
  echo "Singularity option selected, but Docker is being used."
fi

and my pial surfaces are not getting reconstructed. Both lh_pial and rh_pial are 0kb.

4

Hi @Divesh_Thaploo,

In the future, please format your code with the </> button in the text editor. You can see I edited it for you this time.

Does your code proceed to completion without errors? Do you get the freesurfer-surface bold outputs that you requested?

Best,
Steven

5

Yes, it works without errors, and I get the usual generated bold outputs.

6

What files (relative to your output path) are you looking at that are 0 kb? Is it possible they are symlinks?

7

Within this directory: /derivatives/sourcedata/freesurfer/sub-01/surf lh_pial and rh_pial are 0kb and no they are not symlinks.

8

Do other files have normal or abnormal file sizes? Have you tried running freesurfer separately?

9

Rest all other files are okay. Just these two files are different. I did not run freesurfer seperately. Is that what you would recommend or should I just re-run the autorecon 2 and 3?

10

I would try it just to try to isolate the issue.

11 
[Node] Setting-up "fmriprep_25_0_wf.sub_04_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/tmp/work/fmriprep_25_0_wf/sub_04_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
250428-16:22:50,553 nipype.workflow INFO:
         [Node] Executing "autorecon2_vol" <smriprep.interfaces.freesurfer.ReconAll>
250428-16:22:50,572 nipype.interface INFO:
         resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -nogcareg
250428-16:22:50,591 nipype.interface INFO:
         resume recon-all : recon-all -autorecon2-volonly -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -nogcareg

This is from current subject which is being run!!