FSL: FEAT Registration Error

Hello,

I’m running registration on FEAT, and keep getting the same error message:

Feat main script
/bin/cp /tmp/feat_b5ziBY.fsf design.fsf

mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r /usr/local/fsl/doc/images .files/images

/usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/local/fsl/bin/feat /path/to/feat/.feat/design.fsf -D /path/to/feat/.feat -I 1 -init
10261

/usr/local/fsl/bin/fsl_sub -T 68 -l logs -N feat2_pre -j 10261 /usr/local/fsl/bin/feat /path/to/feat/.feat/design.fsf -D /path/to/feat/.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 "/usr/local/fsl/bin/feat" line 312)

FATAL ERROR ENCOUNTERED:
COMMAND:
/usr/local/fsl/bin/fsl_sub -T 68 -l logs -N feat2_pre -j 10261 /usr/local/fsl/bin/feat /path/to/feat/.feat/design.fsf -D //path/to/feat//.feat -I 1 -prestats
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE

I set up the registration through the feat gui.

Thank you!

Hi,

I have met the same problem when running FEAT. Have you figured it out?

Thanks,
Elvire

I had a similar error come up. In my case, I am using func data that was preprocessed with fmriprep, so I turned off the prestats in FEAT and then only did a minimal registration to standard per Jeanette Mumford’s workaround to deal with higher level stats required files… But I can’t get it to run without redoing all the preprocessing…

Here is a full log of the failed FEAT run in case it is helpful.

FSL

Progress Report / Log

Started at Wed Jul 24 17:15:09 PDT 2019

Feat main script

/bin/cp /tmp/feat_uECSDK.fsf design.fsf

/share/software/user/open/fsl/5.0.10/bin/feat_model design

mkdir .files;cp /share/software/user/open/fsl/5.0.10/doc/fsl.css .files;cp -r /share/software/user/open/fsl/5.0.10/doc/images .files/images

/share/software/user/open/fsl/5.0.10/bin/fsl_sub -T 10 -l logs -N feat0_init /share/software/user/open/fsl/5.0.10/bin/feat /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/design.fsf -D /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat -I 1 -init
21997

/share/software/user/open/fsl/5.0.10/bin/fsl_sub -T 46 -l logs -N feat2_pre -j 21997 /share/software/user/open/fsl/5.0.10/bin/feat /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/design.fsf -D /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.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 "/share/software/user/open/fsl/5.0.10/bin/feat" line 312)

FATAL ERROR ENCOUNTERED:
COMMAND:
/share/software/user/open/fsl/5.0.10/bin/fsl_sub -T 46 -l logs -N feat2_pre -j 21997 /share/software/user/open/fsl/5.0.10/bin/feat /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/design.fsf -D /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat -I 1 -prestats
ERROR MESSAGE:
child process exited abnormally
END OF ERROR MESSAGE


Initialisation

/share/software/user/open/fsl/5.0.10/bin/fslmaths /home/groups/cbohon/ERstudy/analysis/fmriprep/fmriprep/sub-105/func/sub-105_task-reappraisal_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.den prefiltered_func_data -odt float
Total original volumes = 164

/share/software/user/open/fsl/5.0.10/bin/fslroi prefiltered_func_data example_func 82 1


Preprocessing:Stage 1

/share/software/user/open/fsl/5.0.10/bin/mainfeatreg -F 6.00 -d /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat -l /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/logs/feat2_pre -R /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_unwarp.html -r /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_reg.html -i /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/example_func.nii.gz -s /share/sw/free/fsl/5.0.6/fsl/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 “/home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat”
Option -l ( logfile )input with argument “/home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/logs/feat2_pre”
Option -R ( html unwarping report ) selected with argument “/home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_unwarp.html”
Option -r ( html registration report ) selected with argument “/home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_reg.html”
Option -i ( main input ) input with argument “/home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/example_func.nii.gz”
Option -s ( standard image ) selected with argument “/share/sw/free/fsl/5.0.6/fsl/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 /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/reg

Error: you have not selected any images to register to!

FATAL ERROR ENCOUNTERED:
COMMAND:
/share/software/user/open/fsl/5.0.10/bin/mainfeatreg -F 6.00 -d /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat -l /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/logs/feat2_pre -R /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_unwarp.html -r /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/report_reg.html -i /home/groups/cbohon/ERstudy/analysis/reappraisal/1stlevel/Run1/sub-105/reappraisal1.feat/example_func.nii.gz -s /share/sw/free/fsl/5.0.6/fsl/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 "/share/software/user/open/fsl/5.0.10/bin/feat" line 312)

Error encountered while running in main feat script, halting.
child process exited abnormally


























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