Summary of what happened:
Dear Experts,
I am running one participant through fMRIprep, but it is not working. I have tried
several times, and the problem is always the same during recon-all. I am out of ideas
about what might be happening. I am using 7T fMRI. Please see the attached crash file and recon-all.log. Do you have any idea what is happening?
Many thanks,
Daniela Valério
Command used (and if a helper script was used, a link to the helper script or the command generated):
export FMRIPREP=/neurospin/unicog/resources/softwares/FMRIPREP/fmriprep-22.0.2.sing
export PROJECT=/home_local/Daniela_fmri_analyses/Participants
export FREESURFER=$FREESURFER_HOME
export SOURCE=BIDS
export DEST=fmriprep
# Print the paths
echo "FMRIPREP: $FMRIPREP"
echo "PROJECT: $PROJECT"
echo "FREESURFER: $FREESURFER"
echo "SOURCE: $SOURCE"
echo "DEST: $DEST"
singularity run --cleanenv \
-B "${PROJECT}: /data" \
-B "${FREESURFER}:/freesurfer" \ ${FMRIPREP} \
"/data/${SOURCE}" \
"/data/$DEST" \
participant \
--participant-label 06\
--output-spaces T1w MNI152NLin2009cAsym\
--bold2t1w-init header\
--bold2t1w-dof 9 \
--fs-license-file "/freesurfer/license.txt" \
-w "/data/${DEST}/work_dir" \
--skip-bids-validation
Version:
22.0.2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Jul 18 11:58:17 CEST 2024
/data/fmriprep/sourcedata/freesurfer/sub-06/mri
mri_normalize -g 1 -seed 1234 -mprage -noconform nu.mgz T1.mgz
using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
not interpolating and embedding volume to be 256^3...
reading mri_src from nu.mgz...
normalizing image...
NOT doing gentle normalization with control points/label
talairach transform
1.27830 -0.07062 -0.02792 -4.15817;
0.08257 1.06935 0.28636 -34.69358;
0.03503 -0.22377 1.19210 19.37392;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 3
Starting OpenSpline(): npoints = 3
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
error: No such file or directory
error: MRInormFindControlPoints: could not find enough control points
error: No such file or directory
error: MRInormFindControlPoints failed
Linux nautilus 5.15.0-107-generic #117-Ubuntu SMP Fri Apr 26 12:26:49 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-06 exited with ERRORS at Thu Jul 18 11:58:31 CEST 2024
Screenshots / relevant information:
recon-all-log.txt (97.7 KB)
crash-20240718-115833-dc277359-autorecon1-42d5d326-c2fb-479f-ad51-15dbf9eb84d3.txt (14.2 KB)
