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This repository has been archived by the owner on Apr 19, 2023. It is now read-only.
#!/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 <file>.dsn
#
# 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=task_$(whoami)
design=/home/dcn/ymm/data/analysis/code/XCP/normal/design/v1.0/task.dsn
sequence=anatomical
standard=MNI%2x2x2
###################################################################
# PIPELINE
###################################################################
pipeline=task,roiquant,norm
###################################################################
# 1 TASK
###################################################################
task_design[1]=task.fsf
task_fmriprep[1]=1
task_rerun[1]=N
task_cleanup[1]=Y
###################################################################
# 2 ROIQUANT
###################################################################
roiquant_atlas[2]=power264
roiquant_globals[2]=1
roiquant_vol[2]=0
roiquant_rerun[2]=0
roiquant_cleanup[2]=1
###################################################################
# 3 NORM
###################################################################
norm_rerun[3]=0
norm_cleanup[3]=1
Error message
Current processing step:
Executing FEAT analysis
····································································
· Preparing environment
· Processing FEAT design:
· /home/dcn/ymm/data/data/BIDS/normal/derivatives/task/sub-NFB01/ses-s1/run-01/task/model/sub-NFB01_ses-s1_run-01_design.fsf
can't read "env(USER)": no such variable
while executing
"set USER $env(USER)"
(file "/opt/fsl-5.0.10/tcl/fslstart.tcl" line 6)
invoked from within
"source $env(FSLDIR)/tcl/fslstart.tcl"
(file "/opt/fsl-5.0.10/bin/feat" line 76)
Runtime Information
Singularity ver. 1.0
The text was updated successfully, but these errors were encountered:
Can't perform task module
I'm performing 'task' module to estimate brain activation but FEAT doesn't go well.
Cohort file
Design File
Error message
Runtime Information
Singularity ver. 1.0
The text was updated successfully, but these errors were encountered: