rhancockn
commented
2 years ago I’ve seen something similar happen when the input T1 has been preprocessed with intensity normalization. Is this the case in your data, eg does the white matter have an intensity of 110?
On Feb 22, 2022, at 11:05 AM, Soichi Hayashi @.***> wrote:
Hello. We are running HCPpipeline docker://bids/hcppipelines:v4.1.3-1. When we feed t1w and t2w input file, we run into the following error message.
Fri Feb 18 18:17:36 EST 2022:T2wToT1wReg.sh: START: T2w2T1Reg Running FAST segmentation Exception: Not enough classes detected to init KMeans Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2 terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2 /usr/local/fsl/bin/epi_reg: line 320: 13055 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_pve_2 -thr 0.5 -bin ${vout}_fast_wmseg Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg /usr/local/fsl/bin/epi_reg: line 329: 13086 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge I think this means that FAST segmentation is failing to generate the output file T2w2T1w_fast_pve_2 because something is not right with the input files. Is that correct? If so, do you have any suggestion on what we should do to troubleshoot this problem?
We are running the container with the following options
https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/main
singularity exec -e \ -B
pwd/bids:/bids \ -Bpwd/output:/output \ docker://bids/hcppipelines:v4.1.3-1 \ ./run.py /bids /output participant \ --n_cpus 8 \ --stages $stage \ --license_key "$FREESURFER_LICENSE" \ --participant_label $sub \ --processing_mode $processing_mode \ $skipbidsvalidation We are running a slightly modified version of run.py for our jobs and here is the current content > https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/run.py— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.
soichih
giulia-berto
ericearl
francopestilli
Hello. We are running HCPpipeline
docker://bids/hcppipelines:v4.1.3-1. When we feed t1w and t2w input file, we run into the following error message.I think this means that FAST segmentation is failing to generate the output file
T2w2T1w_fast_pve_2because something is not right with the input files. Is that correct? If so, do you have any suggestion on what we should do to troubleshoot this problem?We are running the container with the following options
https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/main
We are running a slightly modified version of
run.pyfor our jobs and here is the current content > https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/run.py