Problems building singularity image for fMRIPrep 1.4.0

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

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.

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

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.

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