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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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source space map '' is not an image issue when running xcpengine #444

Closed QuintinFrerichsWUSTL closed 3 years ago

QuintinFrerichsWUSTL commented 3 years ago

Describe the bug What were you trying to do when the crash happened?

Seems like an issue with the anatomical space

Cohort file Paste cohort file between the triple backticks

id0,img
sub-01,/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/sub-01/ses-1/func/sub-01_ses-1_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz

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

#!/usr/bin/env bash

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

###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher 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.
# * MODULE VARIABLES are used during one stage of the analysis.
#                  These are typically array variables with array
#                  indices equal to the index of the module that
#                  calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
#                  These are typically 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=fc_$(whoami)
design=/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/fc-36p.dsn
sequence=anatomical
standard=MNI%2x2x2

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

pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc

###################################################################
# 1 PRESTATS
###################################################################

prestats_rerun[1]=1
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]=0
confound2_censor_contig[2]=0
confound2_rerun[2]=0
confound2_cleanup[2]=1

###################################################################
# 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_smo[3]=6
regress_sptf[3]=susan
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=1
regress_process[3]=DMT-TMP-REG

###################################################################
# 4 FCON
###################################################################

fcon_atlas[4]=all
fcon_metric[4]=corrcoef
fcon_rerun[4]=0
fcon_cleanup[4]=1

###################################################################
# 5 REHO
###################################################################

reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=susan
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1

###################################################################
# 6 ALFF
###################################################################

alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=susan
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1

###################################################################
# 7 ROIQUANT
###################################################################

roiquant_atlas[7]=all
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1

###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=0
norm_cleanup[8]=1

##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1

Error message Paste your error message between the backticks

Constructing a pipeline based on user specifications
····································································
· [D][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/fc-36p.dsn]
INFO: /root/matlab/startup.m does not exist ... creating
· [C][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/cohort.csv]
· [O][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output]
· [M][Executing serially]
····································································
Date: 202104272046
UUID: 778c2470-300e-4d8e-85db-f21d3451f58f

Checking general dependencies
····································································
· Version AFNI           AFNI_21.1.01 
· 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-v1.2.3
· R version              3.3.3 
· R scripting front-end  3.3.3 
· · RNifti version       1.3.0
· · optparse version     1.6.6
· · pracma version       2.3.3
· · 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]
· [/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01]
· [Initialising space mapping]
· [Initialising derivative maps]
· [Initialising atlas system]
· Ingress
· [Native space: sub-01_anatomical]
· [Standard space: MNI]
· [Anatomical space: sub-01_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][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/sub-01.nii.gz]
[O][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats]

urrent processing step:
Ensure matching orientation
····································································
· Input: /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01~TEMP~.nii.gz
· Template: /xcpEngine/space/MNI/MNI-2x2x2.nii.gz
· Output root:
· checking the orientation of img and template
NATIVE:LPI TEMPLATE:LPI
· NOT re-orienting native bcos they are the same

Current processing step:
getting data from fmriprep directory
····································································
cp: cannot stat '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/sub-01/ses-1/func/sub-01_ses-1_desc-confounds_timeseries.tsv': No such file or directory
cp: cannot stat '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/sub-01/ses-1/func/sub-01_ses-1_desc-confounds_timeseries.json': No such file or directory
· checking refvolume and structural orientation
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_referenceVolume.nii.gz does not exist . 
/xcpEngine/core/functions/exec_ants: line 1:   735 Segmentation fault      (core dumped) ${ANTSPATH}/"${@}"
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_struct.nii.gz does not exist . 
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_referenceVolume.nii.gz does not exist . 
/xcpEngine/core/functions/exec_ants: line 1:   746 Segmentation fault      (core dumped) ${ANTSPATH}/"${@}"
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_referenceVolume.nii.gz does not exist . 
/xcpEngine/core/functions/exec_ants: line 1:   757 Segmentation fault      (core dumped) ${ANTSPATH}/"${@}"
· generate mask and referenceVolumeBrain
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_referenceVolume.nii.gz does not exist . 
/xcpEngine/core/functions/exec_ants: line 1:   769 Segmentation fault      (core dumped) ${ANTSPATH}/"${@}"
Cannot open volume /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/sub-01/ses-1/func/sub-01_ses-1_task-rest_desc-brain_mask for reading!
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_mask.nii.gz does not exist . 
 file /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_referenceVolume.nii.gz does not exist . 
/xcpEngine/core/functions/exec_ants: line 1:   783 Segmentation fault      (core dumped) ${ANTSPATH}/"${@}"
Cannot open volume /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_mask for reading!
Cannot open volume /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_mask for reading!
source space map '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_struct.nii.gz' is not an image
· Quality assessment
Error in readNifti(mask1path) : 
  Failed to read image from path /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_segmentation.nii.gz
Calls: readNifti -> .Call
In addition: Warning message:
In readNifti(mask1path) :
  nifti_image_read: failed to find header file for '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/prestats/sub-01_segmentation.nii.gz'
Execution halted
····································································
Processing step complete:
getting data from fmriprep directory

Module complete

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
                  CURRENTLY PROCESSING MODULE:
                         ★ confound2 ★
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
Delegating control to module]

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

[I][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/sub-01.nii.gz]
[O][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2]

Current processing step:
Generating confound matrix
····································································
· Generating temporal mask
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
· [Computing framewise displacement]
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/mc/sub-01_realignment.1D': No such file or directory
Execution halted
· [Selecting quality criteria]
· [Applying framewise threshold to time series]
· [Evaluating data quality]
· relative maximum motion
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/mc/sub-01_relRMS.1D': No such file or directory
Execution halted
· relative mean motion
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/mc/sub-01_relRMS.1D': No such file or directory
Execution halted
The nuisance matrix is being selected base on design files
· Including realignment parameters
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/mc/sub-01_realignment.1D': No such file or directory
Execution halted
· Including csf
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
 cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D': No such file or directory
Execution halted
· Including gsr
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D': No such file or directory
Execution halted
· Including wm
Error in getopt_options(object, args) : 
  Error in getopt(spec = spec, opt = args) : flag "i" requires an argument
Calls: parse_args -> parse_options -> getopt_options
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D': No such file or directory
Execution halted
· [Including 1 derivative(s)]
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D': No such file or directory
Execution halted
· [Including 2 power(s)]
Error in file(file, "rt") : cannot open the connection
Calls: unname -> as.matrix -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D': No such file or directory
Execution halted
····································································
Processing step complete:
Generating confound matrix

Current processing step:
Validating confound model
····································································
/xcpEngine/modules/confound2/confound2.mod: line 490: /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/confound2/sub-01_confmat.1D: No such file or directory
····································································
Processing step complete:
Validating confound model

Module complete

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

[Delegating control to module]

###################################################################
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
#                                                                 #
#  ⊗                CONFOUND REGRESSION MODULE                 ⊗  #
#                                                                 #
#  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  ⊗  #
###################################################################
[I][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/sub-01.nii.gz]
[O][/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/regress]
Design files  
1.000000

Current processing step:
Demeaning and detrending BOLD timeseries
····································································
· [Applying polynomial detrend]
· [Order: 2]
Error in stats::poly(1:(nvol * 2), degree = order) : 
  'degree' must be less than number of unique points
Execution halted

· [A major error has occurred.]
· [The processing stream will now abort.]
· [Preparing diagnostics]
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Module Workflow Map
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· START
· @0.1
· @7
· @7.5a
· @7.5b
· ERROR
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· [An error occurred while processing module regress.]
· [The error was detected at signpost @7.5b.]
· [The most recent command logged was]
· [dmdt.R -d 2 -i /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/sub-01.nii.gz -o /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/regress/sub-01~TEMP~_DMT.nii.gz]
· [For additional details, view the processing log. For improved]
· [diagnostics, increment verbosity using the -t option.]
· []
· [Processing failed to produce required output: /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output/sub-01/regress/sub-01~TEMP~_DMT.nii.gz]
· []
· [stream abort]
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· [Module failure occurred in a number of subjects. They have been]
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Delegating control to module]

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· [Module failure occurred in a number of subjects. They have been]
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· [Module failure occurred in a number of subjects. They have been]
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                         ★ qcfc ★
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generating report

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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. Was running in Docker directly, with the command: sudo docker run --rm -it -v /home/quintin_frerichs/data/functional-connectivity:/home/quintin_frerichs/data/functional-connectivity -v /tmp:/tmp pennbbl/xcpengine:latest -c /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/cohort.csv -d /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/fc-36p.dsn -o /home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/output

Additional context Add any other context about the problem here.

a3sha2 commented 3 years ago

you are using bold ref as input sub-01_ses-1_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz not preproc, that is why the error message

QuintinFrerichsWUSTL commented 3 years ago

I changed my cohort file to be id0,img sub-01,/home/quintin_frerichs/data/functional-connectivity/mdma-fmri-kings/sub-01/ses-1/func/sub-01_ses-1_task-rest _space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, and the issue didn't change

QuintinFrerichsWUSTL commented 3 years ago

Got the issue figured out actually, thanks for the help!