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