another error on the ds002168 example dataset
CogBrainHealthLab opened this issue · comments
not sure if this is the same issue as #266
i'm running Running HippUnfold with Singularity on a CentOS Linux 7 server
the command:
singularity run -e khanlab_hippunfold_latest.sif ds002168 ds002168_hippunfold participant -n --modality T1w --cores 2
i cant paste the full log here as it exceeds the limit for the number of characters, so i'll just paste the start and end of the log
Config file config/snakebids.yml is extended by additional config specified via the command line.
Wildcard constraints in inputs are ignored. (rule: template_xfm_itk2ras)
Building DAG of jobs...
Job stats:
job count
-------------------------------------- -------
affine_gii_to_native 8
all 1
archive_work_after_final 1
calculate_curvature_from_surface1 2
calculate_curvature_from_surface2 2
calculate_gyrification1 2
calculate_gyrification2 4
calculate_surface_area1 2
calculate_surface_area2 4
calculate_thickness_from_surface1 2
calculate_thickness_from_surface2 2
combine_tissue_subfield_labels_corobl 2
compose_template_xfm_corobl 1
compose_warps_native_to_unfold 4
compose_warps_unfold_to_crop_native 4
constrain_surf_to_bbox 14
convert_template_xfm_ras2itk 1
correct_nan_vertices1 6
correct_nan_vertices2 8
cp_template_to_unfold 14
cp_unfolded_noconstrain 4
create_dlabel_cifti_subfields 1
create_dscalar_metric_cifti 5
create_native_coord_ref 4
create_native_crop_ref 2
create_spec_file_dentate 2
create_spec_file_hipp 2
create_unfold_coord_map 2
create_unfold_ref 2
create_warps_dentate 2
create_warps_hipp 2
dentate_skip_unfoldreg 2
download_model 1
equivolume_coords 2
expand_unfolded_warps 4
get_subfield_vols_subj 1
import_t1 1
import_template_shape 1
inject_init_laplace_coords 12
label_subfields_from_vol_coords_corobl 2
laplace_coords_dentate 6
laplace_coords_hipp 6
lr_flip_t1 1
merge_lr_spec_file 2
metric_to_nii 6
n4_t1 1
nii_to_label_gii 2
normalize_curvature1 2
normalize_curvature2 4
plot_subj_subfields 1
prep_equivolume_coords 2
prep_segs_for_greedy 3
qc_nnunet_dice 2
qc_nnunet_f3d 2
qc_reg_to_template 1
qc_subfield 2
qc_subfield_surf 4
reg_to_template 1
reinsert_subject_labels 2
resample_atlas_to_refvol 2
resample_coords_native_crop 14
resample_native_to_crop 2
resample_subfields_native_crop 2
resample_subfields_to_native 2
resample_unfoldreg_subfields 2
run_inference 2
template_shape_inject 2
template_shape_reg 2
template_xfm_itk2ras 1
unflip_init_coords 6
unflip_nnunet_nii 1
unflip_postproc 1
unfolded_registration 2
warp_gii_unfold2corobl1 6
warp_gii_unfold2corobl2 8
warp_gii_unfoldreg 6
warp_t1_to_corobl_crop 2
total 251
[Tue Jan 16 17:28:58 2024]
rule create_unfold_ref:
output: hippunfold/sub-1425/warps/sub-1425_space-unfold_label-dentate_refvol.nii.gz
jobid: 155
reason: Missing output files: hippunfold/sub-1425/warps/sub-1425_space-unfold_label-dentate_refvol.nii.gz
wildcards: subject=1425, autotop=dentate
resources: tmpdir=/tmp
.
.
.
[Tue Jan 16 17:34:36 2024]
rule archive_work_after_final:
input: hippunfold/sub-1425/surf/sub-1425_space-T1w_den-0p5mm_label-hipp_surfaces.spec, hippunfold/sub-1425/surf/sub-1425_space-T1w_den-0p5mm_label-dentate_surfaces.spec, hippunfold/sub-1425/anat/sub-1425_hemi-L_space-cropT1w_desc-subfields_atlas-multihist7_dseg.nii.gz, hippunfold/sub-1425/anat/sub-1425_hemi-R_space-cropT1w_desc-subfields_atlas-multihist7_dseg.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-hipp_desc-equivol_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-hipp_desc-equivol_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-hipp_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-hipp_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-dentate_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-dentate_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-hipp_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-hipp_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-dentate_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-dentate_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz, hippunfold/sub-1425/warps/sub-1425_space-unfold_label-dentate_refvol.nii.gz, hippunfold/sub-1425/anat/sub-1425_hemi-L_space-cropT1w_desc-preproc_T1w.nii.gz, hippunfold/sub-1425/anat/sub-1425_hemi-R_space-cropT1w_desc-preproc_T1w.nii.gz, hippunfold/sub-1425/qc/sub-1425_from-T1w_to-CITI168_regqc.png, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-cropT1w_desc-subfields_atlas-multihist7_dseg.png, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-cropT1w_desc-subfields_atlas-multihist7_dseg.png, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-T1w_den-0p5mm_label-hipp_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-T1w_den-0p5mm_label-dentate_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-T1w_den-0p5mm_label-hipp_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-T1w_den-0p5mm_label-dentate_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/qc/sub-1425_space-cropT1w_desc-subfields_atlas-multihist7_volumes.png, hippunfold/sub-1425/qc/sub-1425_hemi-L_desc-unetf3d_dice.tsv, hippunfold/sub-1425/qc/sub-1425_hemi-R_desc-unetf3d_dice.tsv
output: work/sub-1425_work.tar.gz
jobid: 1
reason: Missing output files: work/sub-1425_work.tar.gz; Input files updated by another job: hippunfold/sub-1425/anat/sub-1425_hemi-L_space-cropT1w_desc-subfields_atlas-multihist7_dseg.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_space-unfold_label-dentate_refvol.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-T1w_den-0p5mm_label-dentate_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-hipp_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-hipp_desc-equivol_coords.nii.gz, hippunfold/sub-1425/anat/sub-1425_hemi-L_space-cropT1w_desc-preproc_T1w.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-cropT1w_desc-subfields_atlas-multihist7_dseg.png, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-hipp_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-hipp_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/qc/sub-1425_from-T1w_to-CITI168_regqc.png, hippunfold/sub-1425/surf/sub-1425_space-T1w_den-0p5mm_label-dentate_surfaces.spec, hippunfold/sub-1425/anat/sub-1425_hemi-R_space-cropT1w_desc-preproc_T1w.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-hipp_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-cropT1w_desc-subfields_atlas-multihist7_dseg.png, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-dentate_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-hipp_desc-equivol_coords.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-R_desc-unetf3d_dice.tsv, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-R_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-R_label-dentate_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/warps/sub-1425_space-unfold_label-hipp_refvol.nii.gz, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-dentate_from-T1w_to-unfold_mode-image_xfm.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-L_desc-unetf3d_dice.tsv, hippunfold/sub-1425/coords/sub-1425_dir-PD_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/qc/sub-1425_space-cropT1w_desc-subfields_atlas-multihist7_volumes.png, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-L_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-L_space-T1w_den-0p5mm_label-hipp_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/coords/sub-1425_dir-IO_hemi-R_space-cropT1w_label-dentate_desc-laplace_coords.nii.gz, hippunfold/sub-1425/anat/sub-1425_hemi-R_space-cropT1w_desc-subfields_atlas-multihist7_dseg.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-T1w_den-0p5mm_label-hipp_desc-subfields_midthickness.surf.png, hippunfold/sub-1425/warps/sub-1425_hemi-L_label-dentate_from-unfold_to-T1w_mode-image_xfm.nii.gz, hippunfold/sub-1425/surf/sub-1425_space-T1w_den-0p5mm_label-hipp_surfaces.spec, hippunfold/sub-1425/coords/sub-1425_dir-AP_hemi-L_space-cropT1w_label-hipp_desc-laplace_coords.nii.gz, hippunfold/sub-1425/qc/sub-1425_hemi-R_space-T1w_den-0p5mm_label-dentate_desc-subfields_midthickness.surf.png
wildcards: subject=1425
resources: tmpdir=/tmp
[Tue Jan 16 17:34:36 2024]
localrule all:
input: work/sub-1425_work.tar.gz
jobid: 0
reason: Input files updated by another job: work/sub-1425_work.tar.gz
resources: tmpdir=/tmp
Job stats:
job count
-------------------------------------- -------
affine_gii_to_native 8
all 1
archive_work_after_final 1
calculate_curvature_from_surface1 2
calculate_curvature_from_surface2 2
calculate_gyrification1 2
calculate_gyrification2 4
calculate_surface_area1 2
calculate_surface_area2 4
calculate_thickness_from_surface1 2
calculate_thickness_from_surface2 2
combine_tissue_subfield_labels_corobl 2
compose_template_xfm_corobl 1
compose_warps_native_to_unfold 4
compose_warps_unfold_to_crop_native 4
constrain_surf_to_bbox 14
convert_template_xfm_ras2itk 1
correct_nan_vertices1 6
correct_nan_vertices2 8
cp_template_to_unfold 14
cp_unfolded_noconstrain 4
create_dlabel_cifti_subfields 1
create_dscalar_metric_cifti 5
create_native_coord_ref 4
create_native_crop_ref 2
create_spec_file_dentate 2
create_spec_file_hipp 2
create_unfold_coord_map 2
create_unfold_ref 2
create_warps_dentate 2
create_warps_hipp 2
dentate_skip_unfoldreg 2
download_model 1
equivolume_coords 2
expand_unfolded_warps 4
get_subfield_vols_subj 1
import_t1 1
import_template_shape 1
inject_init_laplace_coords 12
label_subfields_from_vol_coords_corobl 2
laplace_coords_dentate 6
laplace_coords_hipp 6
lr_flip_t1 1
merge_lr_spec_file 2
metric_to_nii 6
n4_t1 1
nii_to_label_gii 2
normalize_curvature1 2
normalize_curvature2 4
plot_subj_subfields 1
prep_equivolume_coords 2
prep_segs_for_greedy 3
qc_nnunet_dice 2
qc_nnunet_f3d 2
qc_reg_to_template 1
qc_subfield 2
qc_subfield_surf 4
reg_to_template 1
reinsert_subject_labels 2
resample_atlas_to_refvol 2
resample_coords_native_crop 14
resample_native_to_crop 2
resample_subfields_native_crop 2
resample_subfields_to_native 2
resample_unfoldreg_subfields 2
run_inference 2
template_shape_inject 2
template_shape_reg 2
template_xfm_itk2ras 1
unflip_init_coords 6
unflip_nnunet_nii 1
unflip_postproc 1
unfolded_registration 2
warp_gii_unfold2corobl1 6
warp_gii_unfold2corobl2 8
warp_gii_unfoldreg 6
warp_t1_to_corobl_crop 2
total 251
Reasons:
(check individual jobs above for details)
input files updated by another job:
affine_gii_to_native, all, archive_work_after_final, calculate_curvature_from_surface1, calculate_curvature_from_surface2, calculate_gyrification1, calculate_gyrification2, calculate_surface_area1, calculate_surface_area2, calculate_thickness_from_surface1, calculate_thickness_from_surface2, combine_tissue_subfield_labels_corobl, compose_template_xfm_corobl, compose_warps_native_to_unfold, compose_warps_unfold_to_crop_native, constrain_surf_to_bbox, convert_template_xfm_ras2itk, correct_nan_vertices1, correct_nan_vertices2, cp_unfolded_noconstrain, create_dlabel_cifti_subfields, create_dscalar_metric_cifti, create_native_coord_ref, create_native_crop_ref, create_spec_file_dentate, create_spec_file_hipp, create_unfold_coord_map, create_warps_dentate, create_warps_hipp, dentate_skip_unfoldreg, equivolume_coords, expand_unfolded_warps, get_subfield_vols_subj, inject_init_laplace_coords, label_subfields_from_vol_coords_corobl, laplace_coords_dentate, laplace_coords_hipp, lr_flip_t1, merge_lr_spec_file, metric_to_nii, n4_t1, nii_to_label_gii, normalize_curvature1, normalize_curvature2, plot_subj_subfields, prep_equivolume_coords, prep_segs_for_greedy, qc_nnunet_dice, qc_nnunet_f3d, qc_reg_to_template, ...
missing output files:
affine_gii_to_native, archive_work_after_final, calculate_curvature_from_surface1, calculate_curvature_from_surface2, calculate_gyrification1, calculate_gyrification2, calculate_surface_area1, calculate_surface_area2, calculate_thickness_from_surface1, calculate_thickness_from_surface2, combine_tissue_subfield_labels_corobl, compose_template_xfm_corobl, compose_warps_native_to_unfold, compose_warps_unfold_to_crop_native, constrain_surf_to_bbox, convert_template_xfm_ras2itk, correct_nan_vertices1, correct_nan_vertices2, cp_template_to_unfold, cp_unfolded_noconstrain, create_dlabel_cifti_subfields, create_dscalar_metric_cifti, create_native_coord_ref, create_native_crop_ref, create_spec_file_dentate, create_spec_file_hipp, create_unfold_coord_map, create_unfold_ref, create_warps_dentate, create_warps_hipp, dentate_skip_unfoldreg, download_model, equivolume_coords, expand_unfolded_warps, get_subfield_vols_subj, import_t1, import_template_shape, inject_init_laplace_coords, label_subfields_from_vol_coords_corobl, laplace_coords_dentate, laplace_coords_hipp, lr_flip_t1, merge_lr_spec_file, metric_to_nii, n4_t1, nii_to_label_gii, normalize_curvature1, normalize_curvature2, plot_subj_subfields, prep_equivolume_coords, ...
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
not sure if this is the same issue as #266
i'm running Running HippUnfold with Singularity on a CentOS Linux 7 server
the command:
singularity run -e khanlab_hippunfold_latest.sif ds002168 ds002168_hippunfold participant -n --modality T1w --cores 2i cant paste the full log here as it exceeds the limit for the number of characters, so i'll just paste the start and end of the log
I don't see an error here - did you try running without the dry-run (-n) flag? With that flag it is normal to only report what it will do and not actually run anything.
yes indeed that's the case... my bad