bdeck8317
commented
3 years ago @a3sha2
Further description of the issue that may be causing my images to not show up in the task module:
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# ⊗ TASK-CONSTRAINED ACTIVATION MODULE ⊗ #
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[I][/data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopLow/run-1/sub-DP5001_ses-StroopRealStim_StroopLow_run-1.nii.gz]
[O][/data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopLow/run-1/task]
Current processing step:
Localising FEAT design
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/xcpEngine/core/functions/printx: line 2: ${@}: ambiguous redirect
** AFNI converts NIFTI_datatype=4 (INT16) in file /data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopLow/run-1/sub-DP5001_ses-StroopRealStim_StroopLow_run-1.nii.gz to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
NATIVE:LPI TEMPLATE:LPI
· NOT re-orienting native
Current processing step:
getting data from frmiprep directory
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mkdir: cannot create directory ‘/data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopLow/run-1/task/mc’: File exists
· relative maximum motion
· relative mean motion
The template is MNI
xcpEngine only support MNI, PNC and OASIS templates for now
· generate new /data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopLow/run-1/sub-DP5001_ses-StroopRealStim_StroopLow_run-1_spaces.json with spaceMetadata
· Quality assessment
· [Cross-correlation: 0.9221351 ]
· [Coverage: 0.9886942 ]
· [Jaccard coefficient: 0.9000222 ]
· [Dice coefficient: 0.9473807 ]
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Processing step complete:
getting data from frmiprep directory
· Importing analysis variables
· Parsing design and contrasts
· generate confound
/xcpEngine/modules/task/task.mod: line 820: ((: == 1 : syntax error: operand expected (error token is "== 1 ")
Current processing step:
Executing FEAT analysis
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· Preparing environment
· Processing FEAT design:
· /data/xcpOutput/task_data/sub-DP5001/ses-StroopRealStim/StroopHigh/run-1/task/model/sub-DP5001_ses-StroopRealStim_StroopHigh_run-1_design.fsf
invalid command name "toplevel"
while executing
"toplevel .prompt -borderwidth 5"
(procedure "MxPause" line 4)
invoked from within
"MxPause "FEAT setup file is too old to load - sorry!""
(procedure "feat5:load" line 74)
invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
(file "/opt/fsl-5.0.10/bin/feat" line 309)
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Processing step complete:
Executing FEAT analysis
Module completeLet me know your thoughts.
a3sha2
Describe the bug I am attempting to obtain task regressed data from a series of functional images where there are multiple tasks and multiple runs of the same task. The behavior is odd, as the images are created in the task folder but then are deleted. I have the task module on rerun so that I can regress out the task activity. Additionally, the report is not generated.
Cohort file
Design File
Error message
Runtime Information Docker command: docker run -it \ -v /Users/neurouser1/Documents/DP5/xcp/:/data \ pennbbl/xcpengine:latest \ -c /data/cohorts/DP5_task_cohort.csv \ -d /data/xcp_git_repo/xcpEngine/designs/task.dsn \ -o /data/xcpOutput/task_data/ \ -i /data/xcpOutput/task_data/tmp/ \ -t 1 \ -r /data/fmriprep_out/fmriprep/
Additional context