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PennLINC / xcpEngine

Official public repository for the XCP Engine. This tool is deprecated in favor of XCP-D and ASLPrep.
MIT License
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Cortical Thickness Failing #373

Closed pcamach2 closed 2 years ago

pcamach2 commented 4 years ago

I'm trying to run the anat-antsct.dsn design on a single subject and antsCorticalThickness.sh is failing with nonzero code 139.

id0,id1,img
sub-CUGB103,ses-CUGB103A,CUGB/CUGB103A/fmriprep/fmriprep/sub-CUGB103/anat/sub-CUGB103_desc-preproc_T1w.nii.gz
#!/usr/bin/env bash

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
# This design file stores the values of all variables required to
# execute a complete task-free functional connectivity pipeline.
# You may execute the analysis specified in this design file by
# calling (in any bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * GLOBAL VARIABLES are used at all stages of all analyses.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the analysis
#                  stage during which they are used.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are sometimes array variables with array
#                  indices equal to the value of the primary
#                  subject identifier. They will appear only in
#                  localised design files.
###################################################################

###################################################################
# ANALYSIS VARIABLES
###################################################################

analysis=struc-ACCELERATOR
design=/datain/xcpEngineDesigns/anat-antsct.dsn
sequence=anatomical
standard=MNI%1x1x1

###################################################################
# PIPELINE
###################################################################

pipeline=struc,gmd,jlf,roiquant,norm,qcanat

###################################################################
# 1 STRUC
###################################################################

struc_denoise_anat[1]=0
struc_prior_weight[1]=0.25
struc_posterior_formulation[1]='Socrates[1]'
struc_keepBEImages[1]=0
struc_floating_point[1]=0
struc_random_seed[1]=0
struc_bspline[1]=0
struc_fit[1]=0.3
struc_quick[1]=0
struc_seg_priors[1]=1
struc_rerun[1]=0
struc_cleanup[1]=1
struc_process[1]=ACT

###################################################################
# 2 GMD
###################################################################

gmd_rerun[2]=0
gmd_cleanup[2]=1

###################################################################
# 3 JLF
###################################################################

jlf_extract[3]=1 
jlf_keep_warps[3]=1
jlf_quick[3]=0
jlf_cohort[3]=Younger24
jlf_ncpu[3]=2
jlf_parallel[3]=1
jlf_rerun[3]=0
jlf_cleanup[3]=1

###################################################################
# 4 ROIQUANT
###################################################################

roiquant_atlas[4]=all
roiquant_vol[4]=1
roiquant_rerun[4]=0
roiquant_cleanup[4]=1

###################################################################
# 5 NORM
###################################################################

norm_primary[5]=1
norm_rerun[5]=0
norm_cleanup[5]=1

###################################################################
# 6 qcanat
###################################################################

qcanat_gm[6]=Y
qcanat_gm_val[6]=2,4
qcanat_wm[6]=Y
qcanat_wm_val[6]=3
qcanat_csf[6]=Y
qcanat_csf_val[6]=1
qcanat_cort[6]=Y
qcanat_cort_val[6]=4
qcanat_rerun[6]=0
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][/datain/xcpEngineDesigns/anat-antsct.dsn]
INFO: /home/pcamach2/matlab/startup.m does not exist ... creating
· [C][/datain/TestingFork/CUGB/cohort_anat_db.csv]
· [O][/datain/TestingFork/CUGB/xcpEngine]
· [M][Executing serially]
····································································
Date: 202008061445
UUID: 5e19c8e7-e67b-494a-ad87-527d8f60f770

Checking general dependencies
····································································
· Version AFNI           AFNI_20.1.17 
· Version ANTs           3.0.0.0 
· Version FSL            fsl-5.0.10 
· Version C3D            1.1.0 
· Version JQ             jq-1.5
· Version XCP Engine     xcpEngine-v1.2.1
· R version              3.3.3 
· R scripting front-end  3.3.3 
· · RNifti version       1.1.0
· · optparse version     1.6.6
· · pracma version       2.2.9
· · signal version       0.7.6
····································································
All general dependencies are present.

Checking environment
All environmental variables are defined.

Checking module-specific dependencies

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                      XCP ★ ★ ★ ENGINE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ LOCALISER ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                   XCP ENGINE LOCALISER                    ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

Current processing step:
@1 Localising subject metadata...
····································································
· @1.1 [Parsing subject identifiers]
· @1.1a [Creating output directory]
· @1.1b [/datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A]
· @1.2 [Initialising space mapping]
· @1.3 [Initialising derivative maps]
· @1.4 [Initialising atlas system]
· @1.5 Ingress
· @1.5.1 [Native space: sub-CUGB103_ses-CUGB103A_anatomical]
· @1.5.2a [Standard space: MNI]
· @1.5.3a [Anatomical space: sub-CUGB103_ses-CUGB103A_anatomical]
source space map '' is not an image
· @1.5 [Priming analytic audit]
· @1.6 [Priming quality assessment]
····································································
Processing step complete:
Localising subject metadata...

Current processing step:
@2 Localising image
····································································
· @2.1 [Verifying that images are present]
· @2.2 [Conforming and localising images]
                             -   -   -
>> fslchfiletype NIFTI_GZ /datain/TestingFork/CUGB/CUGB103/CUGB103A/fmriprep/fmriprep/sub-CUGB103/anat/sub-CUGB103_desc-preproc_T1w.nii /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/sub-CUGB103_ses-CUGB103A.nii.gz
····································································
Processing step complete:
Localising image

Current processing step:
@3 Localising design
····································································
· @3.1 [Writing localised design]
· @3.2 [Evaluating subject variables]
····································································
Processing step complete:
Localising design

Localiser complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ struc ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]
###################################################################
# ⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗ #
#                                                                 #
#  ⊗               STRUCTURAL PROCESSING MODULE                ⊗  #
#                                                                 #
# ⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗⊗ #
###################################################################

[I][/datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/sub-CUGB103_ses-CUGB103A.nii.gz]
[O][/datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc]
                             -   -   -
>> rln /xcpEngine/space/MNI/MNI-1x1x1.nii.gz /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/template.nii.gz
                             -   -   -
>> rln /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/sub-CUGB103_ses-CUGB103A.nii.gz /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
                             -   -   -
>> 8-6-1
                             -   -   -
>> 8-1
· @0.1 

Current processing step:
@0 Ensure matching orientation
····································································
· @0.1a Input: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
· @0.1b Template: /xcpEngine/space/MNI/MNI-1x1x1.nii.gz
· @0.1c Output root: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_
NATIVE:LPI TEMPLATE:LPI
· @0.1d NOT re-orienting T1w

Current processing step:
@1 ANTs cortical thickness pipeline
····································································
· @1.1a Input: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
· @1.1b Template: /xcpEngine/space/MNI/MNI-1x1x1.nii.gz
· @1.1c Output root: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_
· @1.x Delegating control to ANTsCT
                             -   -   -
>> antsCorticalThickness.sh -d 3 -a /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz -e /xcpEngine/space/MNI/MNI-1x1x1Head.nii.gz -m /xcpEngine/space/MNI/MNI-1x1x1BrainPrior.nii.gz -p /xcpEngine/space/MNI/MNI_priors/MNI-priors-%03d.nii.gz -o /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_ -s nii.gz -t /xcpEngine/space/MNI/MNI-1x1x1.nii.gz -f /xcpEngine/space/MNI/MNI-1x1x1MaskDilated.nii.gz -g 0 -w 0.25 -b Socrates[1] -j 0 -u 0 -v 0 -q 0
WM[4]
WM 4

    Using antsCorticalThickness with the following arguments:
      image dimension         = 3
      anatomical image        = /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
      brain template          = /xcpEngine/space/MNI/MNI-1x1x1Head.nii.gz
      extraction prior        = /xcpEngine/space/MNI/MNI-1x1x1BrainPrior.nii.gz
      extraction reg. mask    = /xcpEngine/space/MNI/MNI-1x1x1MaskDilated.nii.gz
      segmentation prior      = /xcpEngine/space/MNI/MNI_priors/MNI-priors-%03d.nii.gz
      output prefix           = /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_
      output image suffix     = nii.gz
      registration template   = /xcpEngine/space/MNI/MNI-1x1x1.nii.gz

    ANTs parameters:
      metric                  = CC[fixedImage,movingImage,1,4]
      regularization          = 
      transformation          = SyN[0.1,3,0]
      max iterations          = 100x100x70x20

    DiReCT parameters:
      convergence             = [45,0.0,10]
      thickness prior         = 10
      gradient step size      = 0.025
      smoothing sigma         = 1.5

    Other parameters:
      run quick               = 0
      debug mode              = 0
      denoise images          = 0
      float precision         = 0
      use random seeding      = 0
      prior combinations      = WM[4]

---------------------  Running antsCorticalThickness.sh on bi-headnode01  ---------------------

--------------------------------------------------------------------------------------
 Brain segmentation using the following steps:
   1) Register /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_ExtractedTemplateBrain.nii.gz and /xcpEngine/space/MNI/MNI_priors/MNI-priors-%03d.nii.gz to /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
   2) Warp priors to /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
   3) N-tissue segmentation using Atropos and N4
--------------------------------------------------------------------------------------

BEGIN >>>>>>>>>>>>>>>>>>>>
/opt/ants-latest/bin/antsApplyTransforms -d 3 -i /xcpEngine/space/MNI/MNI_priors/MNI-priors-001.nii.gz -o /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPriorWarped001.nii.gz -r /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz -n Gaussian -t /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior1Warp.nii.gz -t /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior0GenericAffine.mat --float 0 --verbose 1
Using double precision for computations.
Input scalar image: /xcpEngine/space/MNI/MNI_priors/MNI-priors-001.nii.gz
Exception caught during reference file reading 

itk::ImageFileReaderException (0x555555c163d0)
Location: "unknown" 
File: /tmp/ants/build/ITKv5-install/include/ITK-5.0/itkImageFileReader.hxx
Line: 139
Description:  Could not create IO object for reading file /xcpEngine/space/MNI/MNI_priors/MNI-priors-001.nii.gz
  Tried to create one of the following:
    BMPImageIO
    BioRadImageIO
    Bruker2dseqImageIO
    GDCMImageIO
    GE4ImageIO
    GE5ImageIO
    GiplImageIO
    HDF5ImageIO
    JPEGImageIO
    JPEG2000ImageIO
    LSMImageIO
    MGHImageIO
    MINCImageIO
    MRCImageIO
    MetaImageIO
    NiftiImageIO
    NrrdImageIO
    PNGImageIO
    StimulateImageIO
    TIFFImageIO
    VTKImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

 file /xcpEngine/space/MNI/MNI_priors/MNI-priors-001.nii.gz
Reference image: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior0GenericAffine.mat (type = AffineTransform)
  2. /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior1Warp.nii.gz (type = DisplacementFieldTransform)
=============================================================================
/opt/ants-latest/bin/antsCorticalThickness.sh: line 257:   760 Segmentation fault      (core dumped) $cmd
ERROR: command exited with nonzero status 139
Command: /opt/ants-latest/bin/antsApplyTransforms -d 3 -i /xcpEngine/space/MNI/MNI_priors/MNI-priors-001.nii.gz -o /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPriorWarped001.nii.gz -r /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz -n Gaussian -t /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior1Warp.nii.gz -t /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_BrainSegmentationPrior0GenericAffine.mat --float 0 --verbose 1

· [A major error has occurred.]
· [The processing stream will now abort.]
· [Preparing diagnostics]
····································································

Module Workflow Map
····································································
· START
· @0.1
· @0
· @0.1a
· @0.1b
· @0.1c
· @0.1d
· @1
· @1.1a
· @1.1b
· @1.1c
· @1.x
· ERROR
····································································

····································································
· [An error occurred while processing module struc.]
· [The error was detected at signpost @1.x.]
· [The most recent command logged was]
· [antsCorticalThickness.sh -d 3 -a /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A~TEMP~.nii.gz -e /xcpEngine/space/MNI/MNI-1x1x1Head.nii.gz -m /xcpEngine/space/MNI/MNI-1x1x1BrainPrior.nii.gz -p /xcpEngine/space/MNI/MNI_priors/MNI-priors-%03d.nii.gz -o /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_ -s nii.gz -t /xcpEngine/space/MNI/MNI-1x1x1.nii.gz -f /xcpEngine/space/MNI/MNI-1x1x1MaskDilated.nii.gz -g 0 -w 0.25 -b Socrates[1] -j 0 -u 0 -v 0 -q 0]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /datain/TestingFork/CUGB/xcpEngine/sub-CUGB103/ses-CUGB103A/struc/sub-CUGB103_ses-CUGB103A_ExtractedBrain0N4.nii.gz]
· []
· [stream abort]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ gmd ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-CUGB103_ses-CUGB103A removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ jlf ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-CUGB103_ses-CUGB103A removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ roiquant ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-CUGB103_ses-CUGB103A removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ norm ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-CUGB103_ses-CUGB103A removed from analysis]
····································································

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ qcanat ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

····································································
· [Module failure occurred in a number of subjects. They have been]
· [removed from further analysis.]
· · [sub-CUGB103_ses-CUGB103A removed from analysis]
····································································
generating report

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                     ANALYSIS COMPLETE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

This error is occurring when running on an HPC via the latest Singularity image of xcpEngine. For context, the fmriprep output is from version 20.1.1. If this is important, I do not have sudo privileges on this machine and the image was built by someone with higher privileges. We have been trying different versions of the xcpEngine both on the HPC with Singularity and on a workstation with Docker and have encountered failure during antsCorticalThickness in both settings. Any help on getting this to run on the HPC would be very much appreciated.

pcamach2 commented 4 years ago

In case this is relevant, I have run into the exact same error using the latest Docker version of xcpEngine and the standard anat-antsct.dsn with a dataset of my own brain from a completely different project that I use to test most of my code. This test data was processed with fmriprep v20.0.7 and I do have sudo privileges on that workstation

a3sha2 commented 4 years ago

@pcamach2 This could be a memory issue. If you are running this via Singularity make sure your system has at least 10GB of RAM.

pcamach2 commented 4 years ago

@a3sha2 The HPC system has 256 GB of RAM, so I don't think that would be the limiting factor considering that other Singularity images have run with greater RAM demands (e.g. fMRIPrep and some of our in-house images that pull well over 20GB at peak). The machine on which Docker was run has 64GB of RAM and has not had memory failure issues with other Docker images.

a3sha2 commented 4 years ago

Also, the T1w output is already n4 corrected and xcp will do n4 again during ANTsCT, can you use raw the T1w image

pcamach2 commented 4 years ago

@a3sha2 would you recommend just running fMRIPrep without N4 going forward, then?

pcamach2 commented 4 years ago

Also, I am trying to run through the tutorial and encountering the same error with the provided test dataset. Was the T1w specified for use in the tutorial also N4 corrected?

a3sha2 commented 4 years ago

Let me try it from our end, it is possible that the problem is from ANTs. Thank you for your patience.

a3sha2 commented 4 years ago

@pcamach2 the failing is due to priors, pull for new docker or singularity image: latest or 1.2.3

pcamach2 commented 4 years ago

@a3sha2 just pulled the 1.2.3 Docker image and attempting to run. I'll keep you updated

pcamach2 commented 4 years ago

The anat-antsct.dsn pipeline now gets to the qcfc portion and fails to find {xcpEngineOutput}/{subject}/norm/{subject}-intensityStd.nii.gz , which later causes DVARS calculation to fail in the functional processing pipeline

a3sha2 commented 4 years ago

Qcfc is for functional not structural

Get Outlook for iOShttps://aka.ms/o0ukef

From: pcamach2 notifications@github.com Sent: Monday, August 10, 2020 7:57:26 PM To: PennBBL/xcpEngine xcpEngine@noreply.github.com Cc: Azeez Adebimpe azeez.adebimpe@outlook.com; Mention mention@noreply.github.com Subject: Re: [PennBBL/xcpEngine] Cortical Thickness Failing (#373)

The anat-antsct.dsn pipeline now gets to the qcfc portion and fails to find {xcpEngineOutput}/{subject}/norm/{subject}-intensityStd.nii.gz , which later causes DVARS calculation to fail in the functional processing pipeline

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/PennBBL/xcpEngine/issues/373#issuecomment-671647357, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACBXECTQIG3CDSDQED52HKTSACCONANCNFSM4PWVL5VQ.

pcamach2 commented 4 years ago

apologies, this error occurred during the qcanat module, which later caused an error in the qcfc module

pcamach2 commented 4 years ago

Here is the error:

Current processing step:
@3 Computing measures of anatomical quality
····································································
· @3.1 Using cortical mask
                             -   -   -
>> ${XCPEDIR}/utils/qcanat.R -i /data/fmriprep/sub-1/anat/sub-1_desc-preproc_T1w.nii.gz -m /data/xcp_output/sub-1/qcanat/sub-1_gmMask.nii.gz -w /data/xcp_output/sub-1/qcanat/sub-1_wmMask.nii.gz -f /data/xcp_output/sub-1/qcanat/sub-1_foreground.nii.gz -c /data/xcp_output/sub-1/qcanat/sub-1_cortexMask.nii.gz
· [Foreground-background energy ratio:   1.457092 ]
· [Signal-to-noise ratio:                2.662513 ]
· [Contrast-to-noise ratio:              0.1596611 ]
· [Cortical contrasts:                   -0.0387296 ]
· [Entropy focus criterion:              0.5915795 ]
· [Grey matter kurtosis:                 1.620098 ]
· [Grey matter skewness:                 0.524175 ]
· [White matter kurtosis:                1.51769 ]
· [White matter skewness:                0.4213613 ]
· [Background kurtosis:                  50.59019 ]
· [Background skewness:                  6.766232 ]
· @3.2 Organising estimates
····································································
Processing step complete:
Computing measures of anatomical quality

Module Workflow Map
····································································
· START
· @1
· @1.1a
· @1.1b
· @1.1a
· @1.1b
· @1.1a
· @1.1b
· @1.1a
· @1.1b
· @2
· @2.1
· @2.2
· @2.3
· @2.4
· @2.5
· @2.6
· @3
· @3.1
· @3.2
· FINISH
····································································
/xcpEngine/core/functions/cleanup: line 3: ((: == 1 : syntax error: operand expected (error token is "== 1 ")

Module complete
generating report
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/plotting/displays.py:99: UserWarning: No contour levels were found within the data range.
  **kwargs)
Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 405, in <module>
    moving = load_img(outdir+'/norm/'+prefix+'_intensityStd.nii.gz')
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/image.py", line 1063, in load_img
    return check_niimg(img, wildcards=wildcards, dtype=dtype)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/_utils/niimg_conversions.py", line 251, in check_niimg
    raise ValueError("File not found: '%s'" % niimg)
ValueError: File not found: '/data/xcp_output/sub-1/norm/sub-1_intensityStd.nii.gz'

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                     ANALYSIS COMPLETE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
pcamach2 commented 4 years ago

The following error occurs during the running fc-aroma.dsn using the struc output from the run in my last comment:

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ qcfc ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗           FUNCTIONAL QUALITY ASSESSMENT MODULE            ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/data/xcp_output/sub-1/sub-1.nii.gz]
[O][/data/xcp_output/sub-1/qcfc]

Current processing step:
@1 Preparing depth map
····································································
· @1.1 Segmentation: /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz
· @1.2 Output: /data/xcp_output/sub-1/qcfc/sub-1_depthMap.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/layerLabels -l /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~ -o /data/xcp_output/sub-1/qcfc/sub-1_depthMap.nii.gz
· @u.1 
                             -   -   -
>> ${XCPEDIR}/utils/unique.R -i /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 1 -uthr 1 -div 1 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz -mul 100 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-1.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 2 -uthr 2 -div 2 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz -mul 200 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-2.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 3 -uthr 3 -div 3 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz -mul 300 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-3.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 4 -uthr 4 -div 4 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz -mul 400 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-4.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 5 -uthr 5 -div 5 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz -mul 500 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-5.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz
· @u.2 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/prestats/sub-1_segmentation.nii.gz -thr 6 -uthr 6 -div 6 -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz
                             -   -   -
>> ImageMath 3 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz MaurerDistance /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz -sub 1 -mul -1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz
· @u.3 
                             -   -   -
>> ${XCPEDIR}/utils/val2pct.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz -m /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz
· @u.4 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz -mul 600 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz -mul 100 -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-class-6.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz
· @u.5 
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-1.nii.gz -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-2.nii.gz -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-3.nii.gz -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-4.nii.gz -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-5.nii.gz -add /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-layerLabels-depth-6.nii.gz /data/xcp_output/sub-1/qcfc/sub-1_depthMap.nii.gz
····································································
Processing step complete:
Preparing depth map

Current processing step:
@2 Aligning depth map
····································································
· @2.1 Resampling to 6mm isotropic: minimally preprocessed
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-pp-rs.nii.gz -inset /data/xcp_output/sub-1/prestats/sub-1_preprocessed.nii.gz -rmode Li
· @2.2 Resampling to 6mm isotropic: denoised
                             -   -   -
>> 5-3-1
                             -   -   -
>> 5-1
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dn-rs.nii.gz -inset /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dn.nii.gz -rmode Li
· @2.4 Aligning depth map to sequence space
                             -   -   -
>> 5-4-1
                             -   -   -
>> 5-1
                             -   -   -
>> 3dresample -dxyz 6 6 6 -prefix /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-onion-rs.nii.gz -inset /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-onion.nii.gz -rmode NN
····································································
Processing step complete:
Aligning depth map

Current processing step:
@3 Preparing summary graphics
····································································
· @3.1 Acquiring arguments
                             -   -   -
>> fslval /data/fmriprep/sub-1/func/sub-1_task-rest_space-T1w_desc-preproc_bold.nii.gz pixdim4
                             -   -   -
>> 0.167*3.000000 
                             -   -   -
>> 0.083*3.000000 
                             -   -   -
>> cp /data/xcp_output/sub-1/confound2/mc/sub-1_dvars-std.1D /data/xcp_output/sub-1/qcfc/sub-1~TEMP~_dvar.1D
                             -   -   -
>> cp /data/xcp_output/sub-1/confound2/mc/sub-1_fd.1D /data/xcp_output/sub-1/qcfc/sub-1~TEMP~_fd.1D
                             -   -   -
>> cp /data/xcp_output/sub-1/confound2/mc/sub-1_relRMS.1D /data/xcp_output/sub-1/qcfc/sub-1~TEMP~_rms1.1D
· @3.2 Generating visuals
                             -   -   -
>> ${XCPEDIR}/utils/voxts.R -i /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-pp-rs.nii.gz,/data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dn-rs.nii.gz -r /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-onion-rs.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1_voxts.png -t DV:/data/xcp_output/sub-1/qcfc/sub-1~TEMP~_dvar.1D:1.5,RMS:/data/xcp_output/sub-1/qcfc/sub-1~TEMP~_rms1.1D:.249000000,FD:/data/xcp_output/sub-1/qcfc/sub-1~TEMP~_fd.1D:.501000000 -n /xcpEngine/atlas/segmentation6/segmentation6NodeNames.txt
Warning messages:
1: Use of `ts$value` is discouraged. Use `value` instead. 
2: Use of `ts$value` is discouraged. Use `value` instead. 
3: Use of `ts$value` is discouraged. Use `value` instead. 
4: Use of `ts$value` is discouraged. Use `value` instead. 
5: Use of `ts$value` is discouraged. Use `value` instead. 
6: Use of `ts$value` is discouraged. Use `value` instead. 
····································································
Processing step complete:
Preparing summary graphics

Current processing step:
@4 Estimating loss of temporal degrees of freedom
····································································
                             -   -   -
>> rm -f /data/xcp_output/sub-1/qcfc/sub-1_tdof.txt
· @4.1 2 nuisance parameters regressed
· @4.3 0 volumes censored
/xcpEngine/modules/qcfc/qcfc.mod: line 263: nSpikesDV: command not found
· @4.4 Total lost tDOF: 2
····································································
Processing step complete:
Estimating loss of temporal degrees of freedom

Current processing step:
@5 Estimating post-processing DVARS
····································································
· @5.1 [Computing DVARS]
                             -   -   -
>> antsApplyTransforms -e 3 -d 3 -i /data/xcp_output/sub-1/norm/sub-1_referenceVolumeBrainStd.nii.gz -r /data/xcp_output/sub-1/prestats/sub-1_struct.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-referenceVolumeBrain.nii.gz -t /data/xcp_output/sub-1/struc/sub-1_TemplateToSubject1GenericAffine.mat -t /data/xcp_output/sub-1/struc/sub-1_TemplateToSubject0Warp.nii.gz
                             -   -   -
>> ${XCPEDIR}/utils/dvars -i /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz -o /data/xcp_output/sub-1/qcfc/sub-1_dvars -s /data/xcp_output/sub-1/qcfc/sub-1~TEMP~ -d 1 -b /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-referenceVolumeBrain.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz -Tperc 25 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-lowerQuartile.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz -Tperc 75 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-upperQuartile.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-upperQuartile.nii.gz -sub /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-lowerQuartile.nii.gz -div 1.34897950039 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-temporalSD.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz -Tar1 /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-temporalAR.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-temporalAR.nii.gz -mul -1 -add 1 -mul 2 -sqrt -mul /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-temporalSD.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-predictedSD.nii.gz
                             -   -   -
>> fslstats /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-predictedSD.nii.gz -k /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> fslnvols /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz
                             -   -   -
>> fslroi /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t-1.nii.gz 0 123
                             -   -   -
>> fslroi /data/xcp_output/sub-1/regress/sub-1_residualised.nii.gz /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t.nii.gz 1 124
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t.nii.gz -sub /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t-1.nii.gz -sqr /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-tdiff-sq.nii.gz
                             -   -   -
>> fslmaths /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t.nii.gz -sub /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-t-1.nii.gz -div /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-predictedSD.nii.gz -sqr /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-tdiff-vox-std.nii.gz
                             -   -   -
>> fslstats -t /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-tdiff-sq.nii.gz -k /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> rm -f /data/xcp_output/sub-1/qcfc/sub-1_dvars-raw.1D
                             -   -   -
>> rm -f /data/xcp_output/sub-1/qcfc/sub-1_dvars-std.1D
                             -   -   -
>> rm -f /data/xcp_output/sub-1/qcfc/sub-1_dvars-vox.1D
                             -   -   -
>> fslstats -t /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-dvars-tdiff-vox-std.nii.gz -k /data/xcp_output/sub-1/qcfc/sub-1~TEMP~-referenceVolumeBrain.nii.gz -M
                             -   -   -
>> ${XCPEDIR}/utils/1dTool.R -i /data/xcp_output/sub-1/qcfc/sub-1_dvars-std.1D -o mean -f /data/xcp_output/sub-1/qcfc/sub-1_dvars-mean.txt
                             -   -   -
>> cp /data/xcp_output/sub-1/confound2/mc/sub-1_relRMS.1D /data/xcp_output/sub-1/qcfc/sub-1~TEMP~_rms.1D
                             -   -   -
>> ${XCPEDIR}/utils/featureCorrelation.R -i /data/xcp_output/sub-1/qcfc/sub-1_dvars-std.1D,/data/xcp_output/sub-1/qcfc/sub-1~TEMP~_rms.1D
····································································
Processing step complete:
Estimating post-processing DVARS

Module Workflow Map
····································································
· START
· @1
· @1.1
· @1.2
· @2
· @2.1
· @2.2
· @2.4
· @3
· @3.1
· @3.2
· @4
· @4.1
· @4.3
· @4.4
· @5
· @5.1
· FINISH
····································································

Module complete
generating report
/xcpEngine/core/report.py:351: UserWarning: loadtxt: Empty input file: "/data/xcp_output/sub-1/fcon/HarvardOxford/sub-1_HarvardOxford_ts.1D"
  prefix+'_'+ii+'_ts.1D')
/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py:393: RuntimeWarning: Mean of empty slice.
  avg = a.mean(axis)
/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/_methods.py:154: RuntimeWarning: invalid value encountered in true_divide
  ret, rcount, out=ret, casting='unsafe', subok=False)
/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py:2526: RuntimeWarning: Degrees of freedom <= 0 for slice
  c = cov(x, y, rowvar)
/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py:2455: RuntimeWarning: divide by zero encountered in true_divide
  c *= np.true_divide(1, fact)
/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py:2455: RuntimeWarning: invalid value encountered in multiply
  c *= np.true_divide(1, fact)
Traceback (most recent call last):
  File "/xcpEngine/core/report.py", line 356, in <module>
    vmax=1, vmin=-1, axes=axs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nilearn/plotting/matrix_plotting.py", line 142, in plot_matrix
    cmap=cmap, **kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/__init__.py", line 1565, in inner
    return func(ax, *map(sanitize_sequence, args), **kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 358, in wrapper
    return func(*args, **kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 358, in wrapper
    return func(*args, **kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/axes/_axes.py", line 5626, in imshow
    im.set_data(X)
  File "/usr/local/miniconda/lib/python3.7/site-packages/matplotlib/image.py", line 699, in set_data
    .format(self._A.shape))
TypeError: Invalid shape () for image data

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#                                                                 #
#  ⊗                     ANALYSIS COMPLETE                     ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
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a3sha2 commented 4 years ago

if you want qcfc to tun completely, you have to include confound2_framewise[2]=fds:0.04,dv:2 in the design file to get necessary parameters. I am not sure if you need that.