Hi Matthew,
The report log reads as follows:
Progress Report / Log
Started at Tue Sep 4 12:40:00 CDT 2018
Feat main script
/bin/cp /tmp/feat_UdHk5X.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 /Users/marcieking/RS/ND61/ND61.feat/design.fsf -D /Users/marcieking/RS/ND61/ND61.feat -I 1 -init
31226
/usr/local/fsl/bin/fsl_sub -T 360 -l logs -N feat2_pre -j 31226 /usr/local/fsl/bin/feat /Users/marcieking/RS/ND61/ND61.feat/design.fsf -D /Users/marcieking/RS/ND61/ND61.feat -I 1 -prestats
Initialisation
/usr/local/fsl/bin/fslmaths /Users/marcieking/RS/ND61/ND61/func/rest1_RPI prefiltered_func_data -odt float
Total original volumes = 216
Deleting 6 volume(s) - BE WARNED for future analysis!
/usr/local/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 6 210
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 105 1
Preprocessing:Stage 1
/usr/local/fsl/bin/mainfeatreg -F 6.00 -d /Users/marcieking/RS/ND61/ND61.feat -l /Users/marcieking/RS/ND61/ND61.feat/logs/feat2_pre -R /Users/marcieking/RS/ND61/ND61.feat/report_unwarp.html -r /Users/marcieking/RS/ND61/ND61.feat/report_reg.html -i /Users/marcieking/RS/ND61/ND61.feat/example_func.nii.gz -n 10 -h /Users/marcieking/RS/ND61/ND61/anat_RPI/T1_RPI_2_brain -w BBR -x 90 -s /usr/local/fsl/data/standard/betsct1_unsmooth -y 12 -z 90 -a /Users/marcieking/RS/ND61/ND61/fieldmap/fieldMap_prepped_final -b /Users/marcieking/RS/ND61/ND61/fieldmap/fieldmap_magnitude_MAG -e 35 -f 10 -g 0.7 -p y- -w BBR
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/Users/marcieking/RS/ND61/ND61.feat"
Option -l ( logfile )input with argument "/Users/marcieking/RS/ND61/ND61.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/Users/marcieking/RS/ND61/ND61.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/Users/marcieking/RS/ND61/ND61.feat/report_reg.html"
Option -i ( main input ) input with argument "/Users/marcieking/RS/ND61/ND61.feat/example_func.nii.gz"
Option -n ( use nonlinear reg ) input with argument "10"
Option -h ( high-res structural image ) selected with argument "/Users/marcieking/RS/ND61/ND61/anat_RPI/T1_RPI_2_brain"
Option -w ( highres dof ) selected with argument "BBR"
Option -x ( highres search ) selected with argument "90"
Option -s ( standard image ) selected with argument "/usr/local/fsl/data/standard/betsct1_unsmooth"
Option -y ( standard dof ) selected with argument "12"
Option -z ( standard search ) selected with argument "90"
Option -a ( fieldmap image ) selected with argument "/Users/marcieking/RS/ND61/ND61/fieldmap/fieldMap_prepped_final"
Option -b ( field ) selected with argument "/Users/marcieking/RS/ND61/ND61/fieldmap/fieldmap_magnitude_MAG"
Option -e ( echo time ) selected with argument "35"
Option -f ( signal loss Threshold ) selected with argument "10"
Option -g ( echo spacing ) selected with argument "0.7"
Option -p ( phase encoding direction ) selected with argument "y-"
Option -w ( highres dof ) selected with argument "BBR"
Registration
/bin/mkdir -p /Users/marcieking/RS/ND61/ND61.feat/reg
This is where the program gets stuck. Let me know if there is anything else that I can send along. Thanks!
Thanks,
Marcie
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