Hello,
I am trying to carry out the FEAT registration workaround from Mumford Brain Stats but am running into the following error when I try to run the full Level 1 analysis (to generate the reg folder and proceed with the workaround):
"Error: you have not selected any images to register to!".
I am encountering this error despite specifying the correct path to the MNI template. I am including the full output from the report log below for reference. Any insight or help on how to address this issue would be greatly appreciated, thank you!
Best,
Sahana
---
Feat main script
/bin/cp /tmp/feat_bLQfhJ.fsf design.fsf
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat_model design
mkdir .files;cp /ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/doc/fsl.css .files;cp -r /ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/doc/images .files/images
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/fsl_sub -T 10 -l logs -N feat0_init /ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/design.fsf -D /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat -I 1 -init
204116
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/fsl_sub -T 37 -l logs -N feat2_pre -j 204116 /ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/design.fsf -D /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat -I 1 -prestats
child process exited abnormally
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat" line 312)
FATAL ERROR ENCOUNTERED:
COMMAND:
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/fsl_sub -T 37 -l logs -N feat2_pre -j 204116 /ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/design.fsf -D /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat -I 1 -prestats
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE
Initialisation
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/fslmaths /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/Level1_withsmoothing/Conditioning1.feat/filtered_func_data prefiltered_func_data -odt float
Total original volumes = 76
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/fslroi prefiltered_func_data example_func 38 1
Preprocessing:Stage 1
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/mainfeatreg -F 6.00 -d /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat -l /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/logs/feat2_pre -R /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_unwarp.html -r /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_reg.html -i /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/example_func.nii.gz -s /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain -y 6 -z 90
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat"
Option -l ( logfile )input with argument "/ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_reg.html"
Option -i ( main input ) input with argument "/ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/example_func.nii.gz"
Option -s ( standard image ) selected with argument "/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain"
Option -y ( standard dof ) selected with argument "6"
Option -z ( standard search ) selected with argument "90"
Registration
/bin/mkdir -p /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/reg
Error: you have not selected any images to register to!
FATAL ERROR ENCOUNTERED:
COMMAND:
/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/mainfeatreg -F 6.00 -d /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat -l /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/logs/feat2_pre -R /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_unwarp.html -r /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/report_reg.html -i /ncf/mclaughlin/stressdevlab/new_fear_pipeline/fear_shapes_collab/Analyses_PO_SK/1001/session2/conditioning/PPI/CentAmyg_Conditioning1_smoothing+.feat/example_func.nii.gz -s /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain -y 6 -z 90
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE
child process exited abnormally
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr arginde..."
(file "/ncf/nrg/sw/apps/fsl-local/5.0.11-centos7/bin/feat" line 312)
Error encountered while running in main feat script, halting.
child process exited abnormally
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