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Error in task module #230

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ymstmshr opened this issue Sep 18, 2019 · 2 comments
Closed

Error in task module #230

ymstmshr opened this issue Sep 18, 2019 · 2 comments

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@ymstmshr
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Can't perform task module
I'm performing 'task' module to estimate brain activation but FEAT doesn't go well.

Cohort file

id0,id1,id2,img,task_design
sub-NFB01,ses-s1,run-01,data/BIDS/normal/derivatives/fmriprep/sub-NFB01/ses-s1/func/sub-NFB01_ses-s1_task-nback_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,data/analysis/code/XCP/normal/task_activity/fsf_files/sub-NFB01/ses-s1/run-01/design.fsf
sub-NFB01,ses-s1,run-02,data/BIDS/normal/derivatives/fmriprep/sub-NFB01/ses-s1/func/sub-NFB01_ses-s1_task-nback_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,data/analysis/code/XCP/normal/task_activity/fsf_files/sub-NFB01/ses-s1/run-02/design.fsf

Design File

#!/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

@a3sha2
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a3sha2 commented Sep 22, 2019

the xcpengine unable to find the event files
add full directory path to the event directory in design.fsf

@ymstmshr
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Thank you very much for your kind help, but I can't correct it yet.

In my 'real' directory, there are EV files like:
"/home/denbo5/ymm/projects/nf/data/BIDS/normal/derivatives/task/EVs/sub-NFB01/ses-s1/run-01/3BK.txt"

In a design.fsf that was created by the task module (/task/model/sub-NFB01_ses-s1_run-01_design.fsf),

# Custom EV file (EV 1)
set fmri(custom1) "/home/dcn/ymm/data/data/BIDS/normal/derivatives/task/EVs/sub-NFB01/ses-s1/run-01/3BK.txt"

I use the following singularity command

singularity run --cleanenv -B /home/denbo5/ymm/projects/nf:/home/dcn/ymm/data ${SIMG} \
	-c /home/dcn/ymm/data/analysis/code/XCP/normal/cohort/task_cohort_N15.csv.NFB01.csv \
	-d /home/dcn/ymm/data/analysis/code/XCP/normal/design/v1.0/task.dsn \
	-o /home/dcn/ymm/data/data/BIDS/normal/derivatives/task \
	-r /home/dcn/ymm/data

Could you tell me if there is anything wrong? Thanks!

@a3sha2 a3sha2 closed this as completed Dec 15, 2019
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