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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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regress module fails at tfilter #209

Closed yvonnio closed 5 years ago

yvonnio commented 5 years ago

Describe the bug What were you trying to do when the crash happened? Regress module crashes, seems to be failing at tfilter.

Cohort file Paste cohort file between the triple backticks

id0,img
sub-9001,/dagher/dagher11/yyau/urgency/fmri_rs/output/fmriprep/sub-9001/func/sub-9001_task-rest_space-T1w_desc-preproc_bold.nii.gz

Design File Paste your entire design (.dsn) file between the triple backticks

#!/usr/bin/env bash
###################################################################
# PIPELINE
###################################################################

pipeline=prestats,confound2,regress
###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=0
prestats_cleanup[1]=1
prestats_process[1]=FMP

###################################################################
# 2 CONFOUND2
###################################################################

confound2_rps[2]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=1 
confound2_censor_contig[2]=0
confound2_framewise[2]=rmss:0.06,dv:2
confound2_rerun[2]=0
confound2_cleanup[2]=0

###################################################################
# 3  REGRESS
###################################################################

regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_sptf[3]=none # we do not want any smoothing
regress_smo[3]=0
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=0
regress_process[3]=TMP-REG

Error message Paste your error message between the backticks

[Detected that xcp is in a container]
Received options: -c /dagher/dagher11/yyau/urgency/fmri_rs/data_bids/cohort.csv -d /dagher/dagher11/yyau/urgency/fmri_rs/scripts/xcp_fc-36p_spkreg_yvonne.dsn -i /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf -o /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp -r /dagher/dagher11/yyau/urgency/fmri_rs/output/fmriprep
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][/dagher/dagher11/yyau/urgency/fmri_rs/scripts/xcp_fc-36p_spkreg_yvonne.dsn]
· [I][/dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf]
· [C][/dagher/dagher11/yyau/urgency/fmri_rs/data_bids/cohort.csv]
· [O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp]
· [M][Executing serially]
····································································

Checking general dependencies
····································································
· Version AFNI           AFNI_19.1.18 
· 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-v1.0
· R version              3.3.3 
· R scripting front-end  3.3.3 
· · RNifti version       0.10.0
· · optparse version     1.6.2
· · pracma version       2.2.5
· · 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:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-9001_anatomical]
· [Standard space: MNI]
· [Anatomical space: sub-9001_anatomical]
source space map '' is not an image
· [Priming analytic audit]
· [Priming quality assessment]
····································································
Processing step complete:
Localising subject metadata...

Current processing step:
Localising image
····································································
· [Verifying that images are present]
· [Conforming and localising images]
····································································
Processing step complete:
Localising image

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

Localiser complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ prestats ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/prestats]

prestats has already run to completion.
Writing outputs...

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ confound2 ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
#                                                                 #
#  ·                   CONFOUND MODEL MODULE                   ·  #
#                                                                 #
#  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  ·  #
###################################################################

[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/confound2]
CONFOUND MODEL MODULE  has been run
 if you change the design file make sure you  set rerun=1

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ regress ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################

[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/regress]
Design files  
0.719000

Current processing step:
Temporally filtering image and confounds
····································································
/xcpEngine/core/functions/filter_temporal: line 115: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
/xcpEngine/core/functions/filter_temporal: line 120: ((: != 0 : syntax error: operand expected (error token is "!= 0 ")
· [butterworth filter]
· [High pass frequency: 0.01]
· [Low pass frequency: 0.08]
/xcpEngine/utils/tfilter: option requires an argument -- 1
Option not recognised: 
___________________________________________________________________

Usage: tfilter -i <input> -o <output> <options>

Compulsory arguments:
 -i : Input timeseries
      The 4D timeseries to which the temporal filter is to
      be applied.

 -o : Output timeseries
      The path to the file where the filtered timeseries
      will be written.

Optional arguments:
 -f : Temporal filter mode [default fft]
      Input can be any of 'gaussian', 'fft', 'butterworth',
      'chebyshev1', 'chebyshev2', or 'elliptic'.
       * FFT-based filters [default] use a fast Fourier
         transform to attenuate frequencies. An FFT-based
         filter may not be suitable for use in designs that
         incorporate iterative motion censoring, since
         it will include interpolated frequencies in its
         calculations.
       * A Gaussian filter uses Gaussian-weighted least-
         squares
       * Chebyshev and elliptic filters more ideally
         discriminate accepted and attenuated frequencies
         than do Butterworth filters, but they introduce
         ripples in either the passband (chebyshev1),
         stopband (chebyshev2), or both (elliptic) that
         result in some signal distortion.

 -h : Highpass frequency [default 0.01]
      The cutoff frequency below which all signal will be
      removed from the timeseries, in Hz. To create a
      bandpass filter, specify a lowpass frequency that is
      higher than the highpass frequency.

 -l : Lowpass frequency [default nyquist]
      The cutoff frequency above which all signal will be
      removed from the timeseries, in Hz.

 -m : Mask
      Filtering is computed only within the specified
      binary mask.

 -n : Temporal mask with interpolation
      Filtering is computed only within the specified
      temporal mask. Outside of the temporal mask, the values
      of the timeseries are interpolated so as to eliminate
      the influence of masked-out time points on the processed
      timeseries (following Power et al., 2014).
-a : TR 
      image time series fro interpolation.

 -r : Filter order [default 1]
      The filter order indicates the number of input samples
      taken under consideration when generating an output
      signal. In general, using a higher-order filter will
      result in a sharper cutoff between accepted and
      attenuated frequencies. For a gentler filter, use a
      lower order.
      (Affects only Butterworth, Chebyshev, and elliptic
      filters.)

 -d : Filter direction [default 2]
      The filter direction indicates whether the input signal
      should be processed in the forward direction only [-d 1]
      or in both forward and reverse directions [-d 2].
      (Affects only Butterworth, Chebyshev, and elliptic
      filters.)

 -p : Pass band ripple [default 1]
      Chebyshev I and elliptic filters allow for sharper
      discrimination between accepted and attenuated
      frequencies at the cost of a 'ripple' in the pass band.
      This ripple results in somewhat uneven retention of
      pass-band frequencies.
      (Affects only Chebyshev I and elliptic filters)

 -s : Stop band ripple [default 1]
      Chebyshev II and elliptic filters allow for sharper
      discrimination between accepted and attenuated
      frequencies at the cost of a 'ripple' in the stop band.
      This ripple results in somewhat uneven removal of
      stop-band frequencies.
      (Affects only Chebyshev II and elliptic filters)

 -1 : 1D timeseries
      A comma separated list of names and paths to files containing
      one-dimensional timeseries, formatted name1:path1,name2:path2
      Each column in the file should represent a separate
      timeseries, and each row should represent a separate time
      point; the number of rows must equal the number of volumes
      present in the primary BOLD timeseries. The same filtering
      regime that was applied to the primary BOLD timeseries will
      be applied to each column of each 1D file

 -t : Trace
      If this flag is set, then any commands called by the
      tfilter routine will be explicitly printed to the
      console or log.

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

Module Workflow Map
····································································
· START
· @0.1
· @2
· @2.2
· @2.3
· @2.5
· @2.8
· @2.12a
· @2.12b
· @2.12c
· ERROR
····································································

····································································
· [An error occurred while processing module regress.]
· [The error was detected at signpost @2.12c.]
· [The most recent command logged was]
· [tfilter -i /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-062055378~TEMP~.nii.gz -o /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-062055378~TEMP~_TMP.nii.gz -a 0.719000 -f butterworth -h 0.01 -l 0.08 -m /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/prestats/sub-9001_mask.nii.gz -r 1 -d 2 -1]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-062055378~TEMP~_TMP.nii.gz]
· []
· [stream abort]
····································································

generating report

Runtime Information How were you running the software? Docker? Singularity? Directly? If Directly, please consider using Docker or Singluarity first before submitting a bug report. Singularity

Additional context Add any other context about the problem here. Singularity command is:

export fmri_rs_dir=/dagher/dagher11/yyau/urgency/fmri_rs

singularity run --cleanenv -B /run/shm:/run/shm -B /dagher/dagher11/yyau/urgency/fmri_rs:/dagher/dagher11/yyau/urgency/fmri_rs \
  /dagher/scratch/yyau/toolbox/xcpEngine.simg \
  -c $fmri_rs_dir/data_bids/cohort.csv \
  -d $fmri_rs_dir/scripts/xcp_fc-36p_spkreg_yvonne.dsn \
  -i $fmri_rs_dir/workingdir/xcp_wf \
  -o $fmri_rs_dir/output/xcp \
  -r $fmri_rs_dir/output/fmriprep
  -t 2
a3sha2 commented 5 years ago

Hi @yvonnio , it look like the time series is missing and I noticed you have ran this subject before, possible not complete it. Can you clear the previous output and start afresh?

yvonnio commented 5 years ago

Thanks for the quick reply! I removed all the xcp output files (in my case: rm -rf $fmri_rs_dir/output/xcp/*) and then re-ran xcp using singularity. Here's my new error log:

[Detected that xcp is in a container]
Received options: -c /dagher/dagher11/yyau/urgency/fmri_rs/data_bids/cohort.csv -d /dagher/dagher11/yyau/urgency/fmri_rs/scripts/xcp_fc-36p_spkreg_yvonne.dsn -i /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf -o /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp -r /dagher/dagher11/yyau/urgency/fmri_rs/output/fmriprep
$XCPEDIR is /xcpEngine

Constructing a pipeline based on user specifications
····································································
· [D][/dagher/dagher11/yyau/urgency/fmri_rs/scripts/xcp_fc-36p_spkreg_yvonne.dsn]
· [I][/dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf]
· [C][/dagher/dagher11/yyau/urgency/fmri_rs/data_bids/cohort.csv]
· [O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp]
· [M][Executing serially]
····································································

Checking general dependencies
····································································
· Version AFNI           AFNI_19.1.18
· 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-v1.0
· R version              3.3.3
· R scripting front-end  3.3.3
· · RNifti version       0.10.0
· · optparse version     1.6.2
· · pracma version       2.2.5
· · 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:
Localising subject metadata...
····································································
· [Parsing subject identifiers]
· [Creating output directory]
· [/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-9001_anatomical]
· [Standard space: MNI]
· [Anatomical space: sub-9001_anatomical]
source space map '' is not an image
· [Priming analytic audit]
· [Priming quality assessment]
····································································
Processing step complete:
Localising subject metadata...

Current processing step:
Localising image
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· [Verifying that images are present]
· [Conforming and localising images]
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Processing step complete:
Localising image

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

Localiser complete

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                  CURRENTLY PROCESSING MODULE:
                         ★ prestats ★
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[Delegating control to module]

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#  ⊗                 FMRI PREPROCESSING MODULE                 ⊗  #
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[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/prestats]

Current processing step:
Ensure matching orientation
····································································
· Input: /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-prestats-359044614~TEMP~.nii.gz
· Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· Output root:
· checking the orientation of img and template
NATIVE:LPI TEMPLATE:RPI
· img and template orientation are not the same
· make it: LPI -> RPI

Current processing step:
getting data from fmriprep directory
····································································
· generate new /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001_spaces.json with spaceMetadata
· Quality assessment
· [Cross-correlation:    0.9790804 ]
· [Coverage:             0.9989878 ]
· [Jaccard coefficient:  0.9748687 ]
· [Dice coefficient:     0.9872744 ]
····································································
Processing step complete:
getting data from fmriprep directory

Module complete

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                  CURRENTLY PROCESSING MODULE:
                         ★ confound2 ★
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[Delegating control to module]

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[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/confound2]

Current processing step:
Generating confound matrix
····································································
· Generating temporal mask
· [Computing framewise displacement]
· [Selecting quality criteria]
· [Quality criterion: rel_rms < .04314000]
· [Quality criterion: dvars < 2]
· [Applying framewise threshold to time series]
· [Evaluating data quality]
· relative maximum motion
· relative mean motion
The nuisance matrix is being selected base on design files
· Including realignment parameters
· Including csf
· Including gsr
· Including wm
· [Including 1 derivative(s)]
· [Including 2 power(s)]
····································································
Processing step complete:
Generating confound matrix

Current processing step:
Validating confound model
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Processing step complete:
Validating confound model

Module complete

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                  CURRENTLY PROCESSING MODULE:
                         ★ regress ★
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[Delegating control to module]

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#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
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[I][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/sub-9001.nii.gz]
[O][/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/regress]
Design files
0.719000

Current processing step:
Temporally filtering image and confounds
····································································
· [butterworth filter]
· [High pass frequency: 0.01]
· [Low pass frequency: 0.08]
· Interpolating over masked-out epochs...
· This will be slow
/dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~.nii.gz
Voxel bin 1 out of 65
/xcpEngine/core/functions/exec_xcp: line 1: 30231 Killed                  ${XCPEDIR}/utils/"${@}"
Error in dumpNifti(impath) :
  Failed to read image from path /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~_TMP_interpol.nii.gz
Calls: dumpNifti -> .Call
In addition: Warning message:
In dumpNifti(impath) :
  nifti_image_read: failed to find header file for '/dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~_TMP_interpol.nii.gz'
Execution halted

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

Module Workflow Map
····································································
· START
· @0.1
· @2
· @2.2
· @2.3
· @2.4.1
· @2.5
· @2.6
· @2.8
· @2.12a
· @2.12b
· @2.12c
· ERROR
····································································

····································································
· [An error occurred while processing module regress.]
· [The error was detected at signpost @2.12c.]
· [The most recent command logged was]
· [tfilter -i /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~.nii.gz -o /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~_TMP.nii.gz -a 0.719000 -f butterworth -h 0.01 -l 0.08 -m /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/prestats/sub-9001_mask.nii.gz -n /dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/confound2/mc/sub-9001_tmask.1D -r 1 -d 2 -1 confmat:/dagher/dagher11/yyau/urgency/fmri_rs/output/xcp/sub-9001/confound2/sub-9001_confmat.1D]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /dagher/dagher11/yyau/urgency/fmri_rs/workingdir/xcp_wf/sub-9001-regress-225596380~TEMP~_TMP.nii.gz]
· []
· [stream abort]
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generating report

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a3sha2 commented 5 years ago

There are issues with your memory and runtime Also, the framewise threshold you selected is to low for TR of 0.719s pls check: https://xcpengine.readthedocs.io/modules/regress.html?highlight=TEmporal%20censoring#temporal-censoring

yvonnio commented 5 years ago

Also, the framewise threshold you selected is to low for TR of 0.719s pls check: https://xcpengine.readthedocs.io/modules/regress.html?highlight=TEmporal%20censoring#temporal-censoring

You're right! This was my mistake. So based on using a required threshold of 0.25mm (Satterthwaite et al. 2013), I presume my fds should be calculated as follows:

fds*TR=0.25
fds=0.25/0.719
fds~=0.347

Now if I update my pipeline to include confound2_framewise[2]=rmss:0.347,dv:2 it seems to all run smoothly with no memory or runtime issue.