MemoryError with fMRIPREP

fmriprep
openneuro

#1

Dear fMRIPREP developers/users

I would love to use fMRIPREP via the app on OpenNeuro. Before uploading all my study data I tried to just upload and analyse one example dataset to see if it would process. However, having tried a few analysis parameters (ranging from relatively simple to more sophisticated analysis options) i keep receiving the same error regarding memory. I’ve copied the parameters from the most stripped-down analysis I tried below, and below that is the resulting log. Can anyone help interpret this error for me?

The data itself is whole-brain 3T EPI acquired using the HCP CMRR multiband sequence with an interleaved slice acquisition (Siemens Prisma scanner). So the EPI file is quite big (1.5Gb). Also I uploaded the matching T1-weighted image of course.

It is my first time using BIDS and fMRIPREP so I do not doubt I have made a newbie error.

Many thanks!
Chris

The parameters are here:

n_cpus: 4
participant_label: 01
anat-only: false
longitudinal: false
use-aroma: false
fs-no-reconall: true
no-submm-recon: true
use-syn-sdc: false
force-syn: false
fs-license-file: /input/data/195398ce0ec7794275bfa6bf6cfb460d/freesurfer-license.txt
low-mem: true
ignore: fieldmaps
output-space: template T1w fsaverage
stop-on-first-crash: true

Here is the log (final part only because full thing has too many characters for this message):

“fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize”.
1526579249969 180517-17:47:29,969 workflow INFO:
1526579249969 [Node] Running “unifize” (“niworkflows.nipype.interfaces.afni.utils.Unifize”), a CommandLine Interface with command:
1526579249969 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz
1526579250254 180517-17:47:30,253 workflow INFO:
1526579250254 [Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.mni_mask”.
1526579252457 180517-17:47:32,456 workflow INFO:
1526579252457 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize”.
1526579254629 180517-17:47:34,628 workflow INFO:
1526579254629 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize”.
1526579254631 180517-17:47:34,630 workflow INFO:
1526579254631 [Node] Running “fixhdr_unifize” (“niworkflows.interfaces.utils.CopyXForm”)
1526579254685 180517-17:47:34,684 workflow INFO:
1526579254685 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize”.
1526579255910 180517-17:47:35,909 workflow INFO:
1526579255910 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass”.
1526579255913 180517-17:47:35,913 workflow INFO:
1526579255913 [Node] Running “skullstrip_second_pass” (“niworkflows.nipype.interfaces.afni.preprocess.Automask”), a CommandLine Interface with command:
1526579255913 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
1526579256103 180517-17:47:36,102 workflow INFO:
1526579256103 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass”.
1526579258608 180517-17:47:38,608 workflow INFO:
1526579258608 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2”.
1526579258611 180517-17:47:38,610 workflow INFO:
1526579258611 [Node] Running “fixhdr_skullstrip2” (“niworkflows.interfaces.utils.CopyXForm”)
1526579258637 180517-17:47:38,636 workflow INFO:
1526579258637 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2”.
1526579259989 180517-17:47:39,988 workflow INFO:
1526579259989 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks”.
1526579259993 180517-17:47:39,992 workflow INFO:
1526579259993 [Node] Running “combine_masks” (“niworkflows.nipype.interfaces.fsl.maths.BinaryMaths”), a CommandLine Interface with command:
1526579259993 fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz
1526579260073 180517-17:47:40,71 workflow INFO:
1526579260073 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks”.
1526579261895 180517-17:47:41,894 workflow INFO:
1526579261895 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.dvars” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/dvars”.
1526579261900 180517-17:47:41,899 workflow INFO:
1526579261900 [Node] Running “dvars” (“niworkflows.nipype.algorithms.confounds.ComputeDVARS”)
1526579262013 180517-17:47:42,12 workflow INFO:
1526579262013 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask”.
1526579262016 180517-17:47:42,15 workflow INFO:
1526579262016 [Node] Running “apply_mask” (“niworkflows.nipype.interfaces.fsl.maths.ApplyMask”), a CommandLine Interface with command:
1526579262016 fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
1526579262118 180517-17:47:42,117 workflow INFO:
1526579262118 [Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.mni_seg”.
1526579262156 180517-17:47:42,154 workflow INFO:
1526579262156 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask”.
1526579263120 180517-17:47:43,119 workflow INFO:
1526579263120 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.boldmask_to_t1w” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/boldmask_to_t1w”.
1526579263125 180517-17:47:43,125 workflow INFO:
1526579263125 [Node] Running “boldmask_to_t1w” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579263126 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_corrected_brain_mask_maths_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/mask_t1w_tfm/ref_image_corrected_brain_mask_maths_trans.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
1526579265094 180517-17:47:45,93 workflow INFO:
1526579265095 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acc_tfm” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/acc_tfm”.
1526579265100 180517-17:47:45,100 workflow INFO:
1526579265100 [Node] Running “acc_tfm” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579265100 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/acc_roi/highres001_BrainExtractionBrain_prob_0_tpmsum_roi.nii.gz --interpolation NearestNeighbor --output highres001_BrainExtractionBrain_prob_0_tpmsum_roi_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt
1526579265205 180517-17:47:45,204 workflow INFO:
1526579265206 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcc_tfm” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/tcc_tfm”.
1526579265212 180517-17:47:45,211 workflow INFO:
1526579265212 [Node] Running “tcc_tfm” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579265212 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/csf_roi/highres001_BrainExtractionMask_eroded.nii.gz --interpolation NearestNeighbor --output highres001_BrainExtractionMask_eroded_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt
1526579265639 180517-17:47:45,637 workflow INFO:
1526579265639 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acc_tfm”.
1526579265775 180517-17:47:45,774 workflow INFO:
1526579265775 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcc_tfm”.
1526579267339 180517-17:47:47,338 workflow INFO:
1526579267339 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acc_msk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/acc_msk”.
1526579267343 180517-17:47:47,342 workflow INFO:
1526579267343 [Node] Running “acc_msk” (“niworkflows.nipype.interfaces.utility.wrappers.Function”)
1526579267386 180517-17:47:47,384 workflow INFO:
1526579267386 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acc_msk”.
1526579267925 180517-17:47:47,925 workflow INFO:
1526579267930 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcc_msk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/tcc_msk”.
1526579267933 180517-17:47:47,933 workflow INFO:
1526579267938 [Node] Running “tcc_msk” (“niworkflows.nipype.interfaces.utility.wrappers.Function”)
1526579267978 180517-17:47:47,977 workflow INFO:
1526579267978 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcc_msk”.
1526579270181 180517-17:47:50,180 workflow INFO:
1526579270182 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.wm_tfm” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/wm_tfm”.
1526579270187 180517-17:47:50,186 workflow INFO:
1526579270187 [Node] Running “wm_tfm” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579270194 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/wm_roi/highres001_BrainExtractionBrain_prob_2_roi.nii.gz --interpolation NearestNeighbor --output highres001_BrainExtractionBrain_prob_2_roi_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt
1526579270718 180517-17:47:50,717 workflow INFO:
1526579270718 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.wm_tfm”.
1526579271061 180517-17:47:51,59 workflow INFO:
1526579271061 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.boldmask_to_t1w”.
1526579271231 180517-17:47:51,231 workflow INFO:
1526579271232 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.csf_tfm” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/csf_tfm”.
1526579271235 180517-17:47:51,235 workflow INFO:
1526579271235 [Node] Running “csf_tfm” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579271235 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/csf_roi/highres001_BrainExtractionBrain_prob_0_roi.nii.gz --interpolation NearestNeighbor --output highres001_BrainExtractionBrain_prob_0_roi_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt
1526579271784 180517-17:47:51,782 workflow INFO:
1526579271784 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.csf_tfm”.
1526579272458 180517-17:47:52,458 workflow INFO:
1526579272459 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.wm_msk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/wm_msk”.
1526579272463 180517-17:47:52,462 workflow INFO:
1526579272470 [Node] Running “wm_msk” (“niworkflows.nipype.interfaces.utility.wrappers.Function”)
1526579272513 180517-17:47:52,511 workflow INFO:
1526579272513 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.wm_msk”.
1526579273941 180517-17:47:53,940 workflow INFO:
1526579273941 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.csf_msk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/csf_msk”.
1526579273945 180517-17:47:53,944 workflow INFO:
1526579273945 [Node] Running “csf_msk” (“niworkflows.nipype.interfaces.utility.wrappers.Function”)
1526579273987 180517-17:47:53,986 workflow INFO:
1526579273987 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.csf_msk”.
1526579273994 180517-17:47:53,993 workflow INFO:
1526579273994 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_mni_trans_wf.mask_mni_tfm” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_mni_trans_wf/mask_mni_tfm”.
1526579273999 180517-17:47:53,998 workflow INFO:
1526579273999 [Node] Running “mask_mni_tfm” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579273999 antsApplyTransforms --default-value 0 --float 1 --input /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_corrected_brain_mask_maths_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_mni_trans_wf/gen_ref/1mm_T1_reference.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt
1526579275633 180517-17:47:55,632 workflow INFO:
1526579275633 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.carpetplot_wf.resample_parc” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/carpetplot_wf/resample_parc”.
1526579275637 180517-17:47:55,637 workflow INFO:
1526579275637 [Node] Running “resample_parc” (“niworkflows.interfaces.fixes.FixHeaderApplyTransforms”), a CommandLine Interface with command:
1526579275637 antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /niworkflows_data/mni_icbm152_nlin_asym_09c/1mm_parc.nii.gz --interpolation MultiLabel --output 1mm_parc_trans.nii.gz --reference-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt --transform /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniInverseComposite.h5
1526579286213 180517-17:48:06,212 workflow INFO:
1526579286213 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.carpetplot_wf.resample_parc”.
1526579288525 180517-17:48:08,523 workflow INFO:
1526579288525 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_mni_trans_wf.mask_mni_tfm”.
1526579301419 180517-17:48:21,418 workflow INFO:
1526579301419 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.dvars”.
1526579302818 180517-17:48:22,817 workflow INFO:
1526579302818 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_reg_wf.bold_to_t1w_transform” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/bold_to_t1w_transform”.
1526579302890 180517-17:48:22,889 workflow INFO:
1526579302890 [Node] Running “bold_to_t1w_transform” (“fmriprep.interfaces.itk.MultiApplyTransforms”)
1526580862736 180517-18:14:22,735 workflow INFO:
1526580862736 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_reg_wf.bold_to_t1w_transform”.
1526580864459 180517-18:14:24,458 workflow INFO:
1526580864459 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_reg_wf.merge” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_reg_wf/merge”.
1526580864535 180517-18:14:24,534 workflow INFO:
1526580864535 [Node] Running “merge” (“fmriprep.interfaces.nilearn.Merge”)
1526580901776 180517-18:15:01,774 workflow INFO:
1526580901776 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_reg_wf.merge”.
1526580985766 180517-18:16:25,766 workflow INFO:
1526580985766 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcompcor” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/tcompcor”.
1526580985769 180517-18:16:25,768 workflow INFO:
1526580985769 [Node] Running “tcompcor” (“fmriprep.interfaces.patches.RobustTCompCor”)
1526580995862 180517-18:16:35,861 workflow INFO:
1526580995862 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.tcompcor”.
1526580997869 180517-18:16:37,868 workflow INFO:
1526580997869 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acompcor” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/acompcor”.
1526580997871 180517-18:16:37,871 workflow INFO:
1526580997871 [Node] Running “acompcor” (“fmriprep.interfaces.patches.RobustACompCor”)
1526580999772 180517-18:16:39,771 workflow INFO:
1526580999772 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.rois_plot” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/rois_plot”.
1526580999778 180517-18:16:39,774 workflow INFO:
1526580999778 [Node] Running “rois_plot” (“niworkflows.interfaces.masks.ROIsPlot”)
1526581011830 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581011830 warnings.warn(“No contour levels were found”
1526581014180 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014180 warnings.warn(“No contour levels were found”
1526581014195 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014195 warnings.warn(“No contour levels were found”
1526581014523 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014523 warnings.warn(“No contour levels were found”
1526581014525 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014525 warnings.warn(“No contour levels were found”
1526581014537 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014537 warnings.warn(“No contour levels were found”
1526581014863 /usr/local/miniconda/lib/python3.6/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
1526581014863 warnings.warn(“No contour levels were found”
1526581015244 180517-18:16:55,243 workflow INFO:
1526581015244 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.acompcor”.
1526581016384 180517-18:16:56,383 workflow INFO:
1526581016384 [Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.rois_plot”.
1526581017104 180517-18:16:57,104 workflow INFO:
1526581017104 [Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.signals” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/signals”.
1526581017107 180517-18:16:57,107 workflow INFO:
1526581017107 [Node] Running “signals” (“niworkflows.nipype.interfaces.nilearn.SignalExtraction”)
1526581092128 180517-18:18:12,128 workflow WARNING:
1526581092128 [Node] Error on “fmriprep_wf.single_subject_01_wf.func_preproc_task_taskname_run_01_wf.bold_confounds_wf.signals” (/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_taskname_run_01_wf/bold_confounds_wf/signals)
1526581094998 Traceback (most recent call last):
1526581094999 File “/usr/local/miniconda/bin/fmriprep”, line 11, in
1526581094999 load_entry_point(‘fmriprep==1.0.14’, ‘console_scripts’, ‘fmriprep’)()
1526581094999 File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 314, in main
1526581095000 fmriprep_wf.run(**plugin_settings)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 595, in run
1526581095000 runner.run(execgraph, updatehash=updatehash, config=self.config)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 168, in run
1526581095000 self._clean_queue(jobid, graph, result=result))
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 227, in _clean_queue
1526581095000 raise RuntimeError("".join(result[‘traceback’]))
1526581095000 RuntimeError: Traceback (most recent call last):
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py”, line 68, in run_node
1526581095000 result[‘result’] = node.run(updatehash=updatehash)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 480, in run
1526581095000 result = self._run_interface(execute=True)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
1526581095000 return self._run_command(execute)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 644, in _run_command
1526581095000 result = self._interface.run(cwd=outdir)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 520, in run
1526581095000 runtime = self._run_interface(runtime)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/nilearn.py”, line 97, in _run_interface
1526581095000 signals.append(masker.fit_transform(self.inputs.in_file))
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/input_data/nifti_maps_masker.py”, line 213, in fit_transform
1526581095000 return self.fit().transform(imgs, confounds=confounds)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/input_data/base_masker.py”, line 176, in transform
1526581095000 return self.transform_single_imgs(imgs, confounds)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/input_data/nifti_maps_masker.py”, line 319, in transform_single_imgs
1526581095000 verbose=self.verbose)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/sklearn/externals/joblib/memory.py”, line 283, in call
1526581095000 return self.func(*args, **kwargs)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/input_data/base_masker.py”, line 98, in filter_and_extract
1526581095000 memory_level=memory_level)(imgs)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/sklearn/externals/joblib/memory.py”, line 283, in call
1526581095000 return self.func(*args, **kwargs)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/input_data/nifti_maps_masker.py”, line 29, in call
1526581095000 mask_img=self.resampled_mask_img)
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/nilearn/regions/signal_extraction.py”, line 270, in img_to_signals_maps
1526581095000 data[maps_mask, :])[0].T
1526581095000 File “/usr/local/miniconda/lib/python3.6/site-packages/scipy/linalg/basic.py”, line 909, in lstsq
1526581095000 resids = np.sum(np.abs(x[n:])**2, axis=0)
1526581095000 MemoryError
1526581095000
1526581095101 Sentry is attempting to send 1 pending error messages
1526581095101 Waiting up to 10 seconds
1526581095101 Press Ctrl-C to quit
1526581108053 Error response from daemon: No such container: d84ac9ff-546f-4310-bacd-60a6e09a11f2-lock
1526581108053 No lock found for d84ac9ff-546f-4310-bacd-60a6e09a11f2

END OF MESSAGE


#2

Hi, thanks for the report. This is a known issue with the signal extraction step with very large datasets. The --low-mem flag will significantly reduce memory consumption during this and a few other steps, at the cost of disk space used by the working directory.


#3

Hi,

Thanks for your reply. Are there also any other known solutions? I tried the low-mem option but it still fails. I’m aware that other people successfully process multiband data using OpenNeuro+fMRIPREP.

Do you know what the memory capacity is? Perhaps I will need to install fMRIPREP on a local machine (if it actually has more memory!) instead of using the OpenNeuro app, although i would prefer the latter option for reproducibility purposes.

Many thanks for your help
Chris


#4

Currently FMRIPREP is using 30Gb virtual machines on OpenNeuro. You could try disabling ICA AROMA, but in general I would recommend trying local hardware. It will help debugging, but also OpenNeuro will go through some refactoring soon and job submissions be limited.

If you run share data on OpenNeuro and run FMRIPREP via Docker locally you will achieve similar level of reproducibility as in the current set up.


#5

Thanks Chris! I have a similar amount of RAM locally but sounds like it’s worth changing to a Docker anyway.

I’ve set it up now with Docker, which starts off ok, but I’m alternately getting one of these two errors each time I try to run it - both related to Freesurfer:

First error:
GNU libc version: 2.23
ERROR: Systems running GNU glibc version greater than 2.15
require a newly formatted license file (it’s free). Please
download a new one from the following page:
http://surfer.nmr.mgh.harvard.edu/registration.html

Second error:
ERROR: no run data found in /out/freesurfer/sub-01/mri. Make sure to
have a volume called 001.mgz in /out/freesurfer/sub-01/mri/orig.

In the first case, I have re-registered and created a new license file. In the second case, it appears not to be creating data in the Freesurfer directory (although it creates data in the out/fmriprep directory just fine)

(if you prefer me to post this as a separate topic, let me know)

Cheers
Chris


#6

yes - lets make a new topic


#7

While you post the new topic please specify more details about the commandline you used and the enviroment (operating system)