Closed mishaberegov closed 2 years ago
What is the input command you provide? Are you only running the surface pipeline? The input to recon-surf alone should be the conformed image (which will be generated during the segmentation).
I am only running the surface pipeline. This is the full command. It worked fine a couple of months ago.
!docker run -v D:/Archieve/segmentation/T1:/T1 \
-v D:/Archieve/segmentation/morphometrics:/morphometrics \
-v D:/Archieve/segmentation/segmentation:/segmentation \
-v D:/Archieve/segmentation/fs60:/fs60 \
--rm fastsurfer_reconsurf:cpu \
--fs_license /fs60/license.txt \
--t1 /T1/{name} \
--seg /segmentation/{name[:-4]}.nii \
--sid {name[:-4]} --sd /morphometrics \
--parallel
I suspect it stops here:
# check for input conformance
cmd="$python ${binpath}../FastSurferCNN/data_loader/conform.py -i $t1 --check_only --verbose"
RunIt "$cmd" $LF
So, the unsegmented anatomical t1 image must be conformed according to the requirements? I mean, it used to not be so.
That is correct. It was recently changed to assure that both the segmentation and intensity image are conformed for recon-all (https://github.com/Deep-MI/FastSurfer/pull/92). You can either provide the already conformed image which fits the segmentation or conform the .nii with the conform.py script.
Closing the issue as this is the expected behaviour and not an error
It checks for the input conformance and doesn't work with the raw T1.nii provided. Therefore it's nearly impossible to use with docker as it's shown in the Docker/README.md.