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Read the voxel size from image with python instead of from log #683

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Merged
m-reuter merged 1 commit into from
Mar 21, 2025
Merged

Read the voxel size from image with python instead of from log #683

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13 changes: 2 additions & 11 deletions recon_surf/recon-surf.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -452,20 +452,11 @@ echo "" | tee -a "$LF"
echo " "
} | tee -a "$LF"

CONFORM_LF=$SUBJECTS_DIR/$subject/scripts/conform.log
if [ "$CONFORM_LF" != /dev/null ] ; then rm -f "$CONFORM_LF" ; fi
echo "Log file for Conform test" > "$CONFORM_LF"

# check for input conformance
cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $t1 --check_only --vox_size min --verbose --log $CONFORM_LF"
cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $t1 --check_only --vox_size min --verbose"
RunIt "$cmd" "$LF"

# look into the CONFORM_LF to find the voxel sizes, the second conform.py call will check the legality of vox_size
vox_size_prefix=" - Voxel Size"
vox_size=$(grep -oE "${vox_size_prefix} [0-9.]+" "$CONFORM_LF")
vox_size="${vox_size:${#vox_size_prefix}}"
# remove the temporary conform_log (all info is also in the recon-surf logfile)
if [ -f "$CONFORM_LF" ]; then rm -f "$CONFORM_LF" ; fi
vox_size=$($python -c "from nibabel import load; print(load('$t1').header.get_zooms()[0])")

# here, we check the correct vox_size by passing it to the next conform, so errors in this line might be caused above
cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $asegdkt_segfile --check_only --vox_size $vox_size --dtype any --verbose"
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