MTL segmentation nifti example?

[svinci...@gmail.com]

Dear ASHS team, 

I am trying to create an ASHS atlas from 29 subjects using ashs_train.sh. I am following the instructions found here: https://sites.google.com/view/ashs-dox/local-ashs/building-an-atlas-for-t2-mri. 

I am getting this error (see below for full log): "Unknown exception caught by convert3d When processing command: -copy-transform"

My current thought is that this error is somehow related to the MTL segmentation nifti being constructed improperly. 

Is there an example of an MTL segmentation nifti that I could look at? Or, where might I find a more detailed description of what the MTL segmentation nifti should contain (e.g., are overlapping ROIs ok? only one ROI at a time? etc.)?

Thanks,

Sophia

P.S. I have also attached example datamanifest and snaplabels files, in case it is helpful.

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svincibo:/media/data/svincibo/app-ashs-train/testcase$ /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_train.sh -D /media/data/svincibo/app-ashs-train/testcase/datamanifest.txt -L /media/data/svincibo/app-ashs-train/testcase/snaplabels.txt -w /media/data/svincibo/app-ashs-train/testcase/workdir/

ashs_train execution log

  timestamp:   Tue Dec 15 15:27:03 EST 2020

  invocation:  /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_train.sh -D /media/data/svincibo/app-ashs-train/testcase/datamanifest.txt -L /media/data/svincibo/app-ashs-train/testcase/snaplabels.txt -w /media/data/svincibo/app-ashs-train/testcase/workdir/

  directory:   /media/data/svincibo/app-ashs-train/testcase

  environment:

    ASHS_LABELFILE=/media/data/svincibo/app-ashs-train/testcase/snaplabels.txt

    ASHS_ROOT=/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta

    ASHS_TRAIN_MANIFEST=/media/data/svincibo/app-ashs-train/testcase/datamanifest.txt

    ASHS_WORK=/media/data/svincibo/app-ashs-train/testcase/workdir

Verified atlas sub-002

Not using SGE or GNU parallel

declare -f ashs_align_t1t2

declare -f ashs_ants_pairwise

declare -f ashs_atlas_adaboost_train

declare -f ashs_atlas_build_template

declare -f ashs_atlas_initialize_directory

declare -f ashs_atlas_organize_final

declare -f ashs_atlas_organize_one

declare -f ashs_atlas_organize_xval

declare -f ashs_atlas_organize_xval_backup07072018

declare -f ashs_atlas_pairwise

declare -f ashs_atlas_register_to_rest

declare -f ashs_atlas_resample_tse_subj

declare -f ashs_atlas_resample_tse_to_template

declare -f ashs_atlas_run_xval

declare -f ashs_atlas_side_vars

declare -f ashs_atlas_vars

declare -f ashs_average_images_normalized

declare -f ashs_check_atlas

declare -f ashs_check_bl_result

declare -f ashs_check_main

declare -f ashs_check_train

declare -f ashs_label_fusion

declare -f ashs_label_fusion_apply

declare -f ashs_registration_qc

declare -f ashs_reslice_to_template

declare -f ashs_segmentation_qc

declare -f ashs_subj_side_vars

declare -f ashs_subj_vars

declare -f ashs_template_pairwise_rigid

declare -f ashs_template_reslice_seg

declare -f ashs_template_side_roi

declare -f ashs_template_single_reg

declare -f ashs_xval_bl

declare -f ashs_xval_loo

declare -f ashs_xval_num

declare -f ashs_xval_prepare_bl_exp

declare -f ashs_xval_vars

declare -f dereflink

declare -f fake_qsub

declare -f get_tmpdir

declare -f gnu_parallel_qsub

declare -f job_progress

declare -f qsubmit_double_array

declare -f qsubmit_single_array

declare -f qsubmit_sync

declare -f qwait

declare -f usage

declare -f vers

****************************************

Starting stage 1: Initialize work directory

****************************************

+ source /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_lib.sh

++ source /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_version.sh

+++ ASHS_VERSION_MAJOR=1

+++ ASHS_VERSION_MINOR=0

+++ ASHS_VERSION_PATCH=0

+++ ASHS_VERSION_NOTE=

+++ ASHS_VERSION_FULL=1.0.0

+++ ASHS_VERSION_DATE=20170915

+++ ASHS_OLDEST_COMPAT_DATE=20170810

++ source /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_common_master.sh

+++ [[ ! -n /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta ]]

++++ uname

+++ ARCH=Linux

+++ ASHS_BIN=/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin

+++ ASHS_ANTS=/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/ants_1042

+++ ASHS_FSL=/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/fsl

++++ /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/c3d -version

++++ grep Version

+++ [[ ! -n Version 1.1.0 ]]

+++ PATH=/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/fsl:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/fsl:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/fsl-6.0.3/bin

++ [[ ! /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_config.sh == /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_config.sh ]]

++ source /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/bin/ashs_config.sh

+++ ASHS_SIDES='left right'

+++ ASHS_MPRAGE_DENOISE=0

+++ ASHS_MPRAGE_SRUPSAMPLE=0

+++ ASHS_MPRAGE_SRUPSAMPLE_FACTOR='1 1 1'

+++ ASHS_TSE_DENOISE=0

+++ ASHS_TSE_SRUPSAMPLE=0

+++ ASHS_TSE_SRUPSAMPLE_FACTOR='1 1 1'

+++ ASHS_TSE_ISO_FACTOR=100x100x500%

+++ ASHS_TSE_ISO_REGION_CROP='20x20x0% 60x60x100%'

+++ ASHS_FLIRT_MULTIMODAL_OPTS='-searchrx -5 5 -searchry -5 5 -searchrz -5 5 -coarsesearch 3 -finesearch 1 -searchcost normmi'

+++ ASHS_TEMPLATE_ANTS_ITER=60x20x0

+++ ASHS_TEMPLATE_STAGES_TOTAL=4

+++ ASHS_TEMPLATE_STAGES_RIGID=1

+++ ASHS_TEMPLATE_ROI_DILATION=10x10x10vox

+++ ASHS_TEMPLATE_ROI_MARGIN=4x4x4vox

+++ ASHS_TEMPLATE_TARGET_RESOLUTION=0.4688x0.4688x0.4688mm

+++ ASHS_TEMPLATE_MASK_THRESHOLD=0.5

+++ ASHS_TARGET_ATLAS_FOR_HISTMATCH=0

+++ ASHS_HISTMATCH_CONTROLS=5

+++ ASHS_PAIRWISE_AFFINE_ITER=60x60x0

+++ ASHS_PAIRWISE_DEFORM_ITER=60x60x20

+++ ASHS_PAIRWISE_CROSSCORR_RADIUS=2x2x2

+++ ASHS_PAIRWISE_ANTS_STEPSIZE=0.25

+++ ASHS_PAIRWISE_ANTS_T1_WEIGHT=0

+++ ASHS_LABEL_SMOOTHING=0.24mm

+++ ASHS_MALF_STRATEGY='Joint[0.1,2]'

+++ ASHS_MALF_PATCHRAD=3x3x1

+++ ASHS_MALF_SEARCHRAD=3x3x1

+++ ASHS_MALF_PADDING=0x0x2

+++ ASHS_EC_DILATION=1

+++ ASHS_EC_TARGET_SAMPLES=100000

+++ ASHS_EC_DRYRUN_SAMPLE_RATE=0.01

+++ ASHS_EC_ITERATIONS=500

+++ ASHS_EC_PATCH_RADIUS=6x6x0

+++ ASHS_EC_MINIMUM_SAMPLES=100

+++ ASHS_EC_QSUB_EXTRA_OPTIONS=

++ [[ -n '' ]]

+ cat

Script: ashs_atlas_initdir_qsub.sh

Root: /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta

Working directory: /media/data/svincibo/app-ashs-train/testcase/workdir

PATH: /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/fsl:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/fsl:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/fsl-6.0.3/bin

+ id=sub-002

+ MYWORK=/media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002

+ WFSL=/media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/flirt_t2_to_t1

+ mkdir -p /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002 /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/flirt_t2_to_t1

+ FILES=($(cat $ASHS_TRAIN_MANIFEST | awk -v id=$id '$1 == id { print $2,$3,$4,$5 }'))

++ cat /media/data/svincibo/app-ashs-train/testcase/datamanifest.txt

++ awk -v id=sub-002 '$1 == id { print $2,$3,$4,$5 }'

+ [[ -n '' ]]

+ /media/data/svincibo/app-ashs-train/testcase/ashs-fastashs_beta/ext/Linux/bin/c3d -type ushort /media/data/svincibo/app-ashs-train/testcase/traindata/t1-swapped.nii -as MPR -o /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/mprage.nii.gz /media/data/svincibo/app-ashs-train/testcase/traindata/t2.nii -o /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/tse.nii.gz -popas REF -push REF /media/data/svincibo/app-ashs-train/testcase/traindata/ROI_l_hip.nii -copy-transform -o /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/seg_left.nii.gz -push REF /media/data/svincibo/app-ashs-train/testcase/traindata/ROI_r_hip.nii -copy-transform -o /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/seg_right.nii.gz -push MPR -smooth-fast 4vox -resample 12.5% -o /media/data/svincibo/app-ashs-train/testcase/workdir/atlas/sub-002/mprage_lr.nii.gz

Unknown exception caught by convert3d

  When processing command: -copy-transform

/media/data/svincibo/app-ashs-train/testcase/workdir /media/data/svincibo/app-ashs-train/testcase

STAGE 1: missing file atlas/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat

STAGE 1: missing file atlas/sub-002/seg_left.nii.gz

STAGE 1: missing file atlas/sub-002/seg_right.nii.gz

/media/data/svincibo/app-ashs-train/testcase

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VALIDITY CHECK AT STAGE 1 FOUND 3 ERRORS AND 0 WARNINGS

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