Problems building singularity image for fMRIPrep 1.4.0

dlevitas · May 22, 2019, 1:27pm

Hi,

I’m trying to install the latest version but running into a problem. I’m using docker on my local machine to pull the image and then convert it to singularity. I can pull the image with no trouble, but when I try to convert it to a singularity container, I get this error (truncated):

tar: opt/freesurfer/bin/kww_setup: Cannot open: No error information
tar: opt/freesurfer/bin/label2flat: Cannot open: No error information
tar: opt/freesurfer/bin/label2patch: Cannot open: No error information
tar: opt/freesurfer/bin/label_area: Cannot open: No error information
tar: opt/freesurfer/bin/label_border: Cannot open: No error information
tar: opt/freesurfer/bin/label_child: Cannot open: No error information
tar: opt/freesurfer/bin/label_elderly_subject: Cannot open: No error information
tar: opt/freesurfer/bin/label_subject: Cannot open: No error information
tar: opt/freesurfer/bin/label_subject_flash: Cannot open: No error information
tar: opt/freesurfer/bin/label_subject_mixed: Cannot open: No error information
tar: opt/freesurfer/bin/labels_disjoint: Cannot open: No error information
tar: opt/freesurfer/bin/labels_intersect: Cannot open: No error information
tar: opt/freesurfer/bin/labels_union: Cannot open: No error information
tar: opt/freesurfer/bin/list_otl_labels: Cannot open: No error information
tar: opt/freesurfer/bin/longHippoSubfieldsT1.sh: Cannot open: No error information
tar: opt/freesurfer/bin/long_create_base_sigma: Cannot open: No error information
tar: opt/freesurfer/bin/long_create_orig: Cannot open: No error information
tar: opt/freesurfer/bin/long_mris_slopes: Cannot open: No error information
tar: opt/freesurfer/bin/long_qdec_table: Cannot open: No error information
tar: opt/freesurfer/bin/long_stats_combine: Cannot open: No error information
tar: opt/freesurfer/bin/long_stats_slopes: Cannot open: No error information
tar: opt/freesurfer/bin/long_stats_tps: Cannot open: No error information
tar: opt/freesurfer/bin/long_submit_jobs: Cannot open: No error information
tar: opt/freesurfer/bin/long_submit_postproc: Cannot open: No error information
tar: opt/freesurfer/bin/lpcregister: Cannot open: No error information
tar: opt/freesurfer/bin/lta_convert: Cannot open: No error information
tar: opt/freesurfer/bin/lta_diff: Cannot open: No error information
tar: opt/freesurfer/bin/make-segvol-table: Cannot open: No error information
tar: opt/freesurfer/bin/make_average_subcort: Cannot open: No error information
tar: opt/freesurfer/bin/make_average_subject: Cannot open: No error information
tar: opt/freesurfer/bin/make_average_surface: Cannot open: No error information
tar: opt/freesurfer/bin/make_average_volume: Cannot open: No error information
tar: opt/freesurfer/bin/make_cortex_label: Cannot open: No error information
tar: opt/freesurfer/bin/make_folding_atlas: Cannot open: No error information
tar: opt/freesurfer/bin/make_hemi_mask: Cannot open: No error information
tar: opt/freesurfer/bin/make_symmetric: Cannot open: No error information
tar: opt/freesurfer/bin/make_upright: Cannot open: No error information
tar: opt/freesurfer/bin/makevol: Cannot open: No error information
tar: opt/freesurfer/bin/map_all_labels: Cannot open: No error information
tar: opt/freesurfer/bin/map_all_labels-lh: Cannot open: No error information
tar: opt/freesurfer/bin/map_central_sulcus: Cannot open: No error information
tar: opt/freesurfer/bin/map_to_base: Cannot open: No error information
tar: opt/freesurfer/bin/mcparams2reg: Cannot open: No error information
tar: opt/freesurfer/bin/meanfilter_test: Cannot open: No error information
tar: opt/freesurfer/bin/meanfilter_test_cuda: Cannot open: No error information
tar: opt/freesurfer/bin/meanval: Cannot open: No error information
tar: opt/freesurfer/bin/merge_stats_tables: Cannot open: No error information
tar: opt/freesurfer/bin/mergeseg: Cannot open: No error information
tar: opt/freesurfer/bin/minc2seqinfo: Cannot open: No error information
tar: opt/freesurfer/bin/misc.py: Cannot open: No error information
tar: opt/freesurfer/bin/mkcontrast2m.glnxa64: Cannot open: No error information
tar: opt/freesurfer/bin/mkfsdist: Cannot open: No error information
tar: opt/freesurfer/bin/mkheadsurf: Cannot open: No error information
tar: opt/freesurfer/bin/mkima_index.tcl: Cannot open: No error information
tar: opt/freesurfer/bin/mkmnc_index.tcl: Cannot open: No error information
tar: opt/freesurfer/bin/mksubjdirs: Cannot open: No error information
tar: opt/freesurfer/bin/mksurfatlas: Cannot open: No error information
tar: opt/freesurfer/bin/mkxsubjreg: Cannot open: No error information
tar: opt/freesurfer/bin/mni152reg: Cannot open: No error information
tar: opt/freesurfer/bin/morph_only_subject: Cannot open: No error information
tar: opt/freesurfer/bin/morph_only_subject-lh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_only_subject-rh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_rgb-lh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_rgb-rh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_subject: Cannot open: No error information
tar: opt/freesurfer/bin/morph_subject-lh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_subject-rh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_subject_on_seychelles: Cannot open: No error information
tar: opt/freesurfer/bin/morph_tables-lh: Cannot open: No error information
tar: opt/freesurfer/bin/morph_tables-rh: Cannot open: No error information
tar: opt/freesurfer/bin/mpr2mni305: Cannot open: No error information
tar: opt/freesurfer/bin/mri-func2sph: Cannot open: No error information
tar: opt/freesurfer/bin/mri-funcvits: Cannot open: No error information
tar: opt/freesurfer/bin/mri-sph2surf: Cannot open: No error information
tar: opt/freesurfer/bin/mri2nc: Cannot open: No error information
tar: opt/freesurfer/bin/mriMarkLabelBorderVoxelTest: Cannot open: No error information
tar: opt/freesurfer/bin/mriMarkLabelBorderVoxelTest_cuda: Cannot open: No error information
tar: opt/freesurfer/bin/mriVoxInLabelPartialVolumeTest: Cannot open: No error information
tar: opt/freesurfer/bin/mriVoxInLabelPartialVolumeTest_cuda: Cannot open: No error information
tar: opt/freesurfer/bin/mri_add_new_tp: Cannot open: No error information
tar: opt/freesurfer/bin/mri_add_xform_to_header: Cannot open: No error information
tar: opt/freesurfer/bin/mri_align_long.csh: Cannot open: No error information
tar: opt/freesurfer/bin/mri_and: Cannot open: No error information
tar: opt/freesurfer/bin/mri_annotation2label: Cannot open: No error information
tar: opt/freesurfer/bin/mri_aparc2aseg: Cannot open: No error information
tar: opt/freesurfer/bin/mri_aparc2wmseg: Cannot open: No error information
tar: opt/freesurfer/bin/mri_apply_autoencoder: Cannot open: No error information
tar: opt/freesurfer/bin/mri_apply_bias: Cannot open: No error information
tar: opt/freesurfer/bin/mri_apply_inu_correction: Cannot open: No error information
tar: opt/freesurfer/bin/mri_aseg_edit_reclassify: Cannot open: No error information
tar: opt/freesurfer/bin/mri_aseg_edit_train: Cannot open: No error information
tar: opt/freesurfer/bin/mri_auto_fill: Cannot open: No error information
tar: opt/freesurfer/bin/mri_average: Cannot open: No error information
tar: opt/freesurfer/bin/mri_bc_sc_bias_correct: Cannot open: No error information
tar: opt/freesurfer/bin/mri_binarize: Cannot open: No error information
tar: opt/freesurfer/bin/mri_binarize.bin: Cannot open: No error information
tar: opt/freesurfer/bin/mri_brain_volume: Cannot open: No error information
tar: opt/freesurfer/bin/mri_build_priors: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_label: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_normalize: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_register: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_register_cuda: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_tissue_parms: Cannot open: No error information
tar: opt/freesurfer/bin/mri_ca_train: Cannot open: No error information
tar: opt/freesurfer/bin/mri_cal_normalize: Cannot open: No error information
tar: opt/freesurfer/bin/mri_cal_renormalize_gca: Cannot open: No error information
tar: opt/freesurfer/bin/mri_cc: Cannot open: No error information
tar: opt/freesurfer/bin/mri_cht2p: Cannot open: No error information
tar: opt/freesurfer/bin/mri_classify: Cannot open: No error information
tar: opt/freesurfer/bin/mri_cnr: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compile_edits: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_bias: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_change_map: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_distances: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_layer_fractions: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_overlap: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_seg_overlap: Cannot open: No error information
tar: opt/freesurfer/bin/mri_compute_structure_transforms: Cannot open: No error information

I’ve never had an issue converting to singularity, so I’m wondering if there’s something new with version 1.4.0 that I need to be aware of during installation?

Thanks,
Dan

oesteban · May 22, 2019, 3:30pm

In principle you should be able to create the image. What exact command are you running?

One easy first shot would be cleaning up singularity’s cache.

kaczmarj · May 22, 2019, 4:30pm

One easy first shot would be cleaning up singularity’s cache.

I agree. I also set my singularity cache to a temporary location:

export SINGULARITY_CACHEDIR="/dev/shm/$(whoami)/singularity"

dlevitas · May 22, 2019, 6:22pm

Thanks @oesteban @kaczmarj. Setting my singularity cache to temp space fixed the issue.

yarikoptic · May 22, 2019, 7:06pm

FWIW, there are auto-converted to singularity images for all BIDS apps (recent versions only ATM) available from https://www.singularity-hub.org/collections/2761 .
For fmriprep there is 1.4.0 image (shub://ReproNim/containers:bids-fmriprep–1.4.0). 1.4.1 was not yet released – only a rc, and I decided to skip those for now in this effort.
If you are into git/git-annex/DataLad – all of those are also available within https://github.com/ReproNim/containers/ DataLad dataset, which comes also with a helper for singularity to assist in avoiding side-effects from the host environment.