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Dear infantFS-team,
We are a team of PhD students, who recently decided to use infantFS for the
segmentation and surface extraction on our data.
We used the infant_recon_all command for preprocessing T1w sMRI scans from the
Baby Connectome Project dataset. The pipeline runs without any errors, but we
encountered noticeable inaccuracies in the reconstructed surfaces, especially
concerning the pial surface. The white matter surface reconstruction was mostly
accurate (with some exceptions), but in some cases even the segmentation fails
as well, particularly in very young subjects.
Even when the segmentation is accurate, the reconstruction of the pial surface
fails to align correctly with the grey matter boundaries, often (if not always)
in the medial temporal lobes. All scans have undergone quality control to
include only those with minimal motion artefacts. The age range of the subjects
analysed, spans from 0 to 4 years old. All scans were realigned and
intensity-corrected using the iBEAT toolbox.
We would gladly appreciate any assistance in understanding the causes of this
problem and are looking forward to methods or changes that we need to follow in
order to solve them. Attached you can find the script we used for the analysis
of the scans in a .txt form. Please feel free to ask for any further
information, details or materials regarding this issue.
Thanks a lot in advance for your time and help!
Best regards
Thanos Tsigaras
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Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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#!/bin/bash
INFANTFS_IMG="path/to/infantFS/image"
FS_LICENSE="path/to/freesurfer/license"
export SUBJECTS_DIR="path/to/data/parent/folder"
if [[ $2 -ge 0 && $2 -lt 6 ]]; then
FLAG="--newborn"
elif [[ $2 -ge 6 && $2 -lt 14 ]]; then
FLAG="--oneyear"
else
FLAG=""
fi
singularity exec \
-B $FS_LICENSE:/opt/freesurfer/.license \
-B $SUBJECTS_DIR:/outgoing/ \
$INFANTFS_IMG infant_recon_all --s $1 --age $2 $FLAG
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