Dear FSL experts,
I cannot find an explantation for the error in my FEAT Preprocessing Analysis. Can somebody help me to understand why the Registration does not work? I applied fslreorient2std to my 4D file, MPrage and even the Fieldmap. I applied Bet on Mprage as described on FSL Homepage and got the field map with fslprepare, also as described on the homepage.
I also do not think that my computer is running out of RAM cause we let run the Preprocessing also on our server. But still, all the time this error occurs:
overlay 0 0 FM_UD_fmap_mag_brain2str -a ../example_func2highres_fast_wmedge 0.001 5 fieldmap2edges
/usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fieldmap2edges.png; rm sl?.png
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sh: line 1: 5175 Segmentation fault: 11 /usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
Cannot open sla.png for reading
rm: sl?.png: No such file or directory
Please see below the full Report!
Your help is highly appreciated!
Kind Regards,
Eva
Progress Report / Log
Started at Tue Dec 19 08:46:06 CET 2017
Feat main script
/bin/cp /tmp/feat_hF88AT.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/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/design.fsf -D /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat -I 1 -init
3469
/usr/local/fsl/bin/fsl_sub -T 246 -l logs -N feat2_pre -j 3469 /usr/local/fsl/bin/feat /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/design.fsf -D /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat -I 1 -prestats
3560
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 3560 /usr/local/fsl/bin/feat /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/design.fsf -D /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat -stop
Initialisation
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_002_mr_ep2d_96x96_32Channel_painreward_20160808/FMS_01_20160808_001_002_mr_ep2d_96x96_32Channel_painreward_reoriented prefiltered_func_data -odt float
Total original volumes = 460
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 230 1
Preprocessing:Stage 1
/usr/local/fsl/bin/mainfeatreg -F 6.00 -d /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat -l /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/logs/feat2_pre -R /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/report_unwarp.html -r /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/report_reg.html -i /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/example_func.nii.gz -h /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_20160808/FMS_01_20160808_001_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_swapdim_brain -w BBR -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -a /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_reoriented_rads -b /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_mag_reoriented_brain -e 30 -f 10 -g 0.37 -p y- -w BBR
Option -F ( FEAT version parameter ) selected with argument "6.00"
Option -d ( output directory ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat"
Option -l ( logfile )input with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/logs/feat2_pre"
Option -R ( html unwarping report ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/report_unwarp.html"
Option -r ( html registration report ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/report_reg.html"
Option -i ( main input ) input with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/example_func.nii.gz"
Option -h ( high-res structural image ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_20160808/FMS_01_20160808_001_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_swapdim_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/MNI152_T1_2mm_brain"
Option -y ( standard dof ) selected with argument "12"
Option -z ( standard search ) selected with argument "90"
Option -a ( fieldmap image ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_reoriented_rads"
Option -b ( field ) selected with argument "/Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_mag_reoriented_brain"
Option -e ( echo time ) selected with argument "30"
Option -f ( signal loss Threshold ) selected with argument "10"
Option -g ( echo spacing ) selected with argument "0.37"
Option -p ( phase encoding direction ) selected with argument "y-"
Option -w ( highres dof ) selected with argument "BBR"
Registration
/bin/mkdir -p /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01.feat/reg
/usr/local/fsl/bin/fslmaths ../example_func EF_D_example_func
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_reoriented_rads FM_UD_fmap
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_mag_reoriented_brain FM_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_fieldmap_mag_reoriented FM_UD_fmap_mag
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -V | awk '{ print $1 }'
106243
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print $1 }'
470016
0.226041
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -bin FM_UD_fmap_mag_brain_mask -odt short
/usr/local/fsl/bin/fslmaths FM_UD_fmap -abs -bin -mas FM_UD_fmap_mag_brain_mask -mul -1 -add 1 -bin FM_UD_fmap_mag_brain_mask_inv
/usr/local/fsl/bin/cluster -i FM_UD_fmap_mag_brain_mask_inv -t 0.5 --no_table -o FM_UD_fmap_mag_brain_mask_idx
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain_mask_idx -R | awk '{ print $2 }'
230.000000
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_idx -thr 230.000000 -bin -mul -1 -add 1 -bin -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain_mask
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
0.623596
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub 0.623596 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -P 98
988.550110
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -thr 494.275 -bin FM_UD_fmap_mag_brain_mask50
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_mag_brain_mask50 -thr 0.5 -bin FM_UD_fmap_mag_brain_mask
/usr/local/fsl/bin/fslmaths FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
/usr/local/fsl/bin/fugue --loadfmap=FM_UD_fmap --savefmap=FM_UD_fmap_tmp_fmapfilt --mask=FM_UD_fmap_mag_brain_mask --despike --despikethreshold=2.1
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub FM_UD_fmap_tmp_fmapfilt -mas FM_UD_fmap_mag_brain_mask_ero -add FM_UD_fmap_tmp_fmapfilt FM_UD_fmap
/bin/rm -f FM_UD_fmap_tmp_fmapfilt* FM_UD_fmap_mag_brain_mask_ero* FM_UD_fmap_mag_brain_mask50* FM_UD_fmap_mag_brain_i*
/usr/local/fsl/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
-0.623596
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -0.623596 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
/usr/local/fsl/bin/fslstats FM_UD_fmap -R | awk '{ print $1 }'
-1196.628906
/usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -1196.628906 -add 10 -mas FM_UD_fmap_mag_brain_mask grot
/usr/local/fsl/bin/fslstats grot -l 1 -p 0.1 -p 95
318.666504 1480.375732
/usr/local/fsl/bin/overlay 0 0 FM_UD_fmap_mag -a grot 318.666504 1480.375732 fmap+mag
/usr/local/fsl/bin/slicer fmap+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fmap+mag.png; rm sl?.png
/usr/local/fsl/bin/sigloss -i FM_UD_fmap --te=0.03 -m FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss
/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain FM_UD_fmap_mag_brain_siglossed -odt float
/usr/local/fsl/bin/fslmaths FM_UD_fmap_sigloss -thr 0.9 FM_UD_fmap_sigloss -odt float
/usr/local/fsl/bin/overlay 1 0 FM_UD_fmap_mag_brain -a FM_UD_fmap_sigloss 0 1 FM_UD_sigloss+mag
/usr/local/fsl/bin/slicer FM_UD_sigloss+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_sigloss+mag.png; rm sl?.png
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_20160808/FMS_01_20160808_001_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_swapdim_brain highres
/usr/local/fsl/bin/fslmaths /Users/eva/Documents/1_Studium/Psychologie_Master/Masterarbeit/FMS_01/1_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_20160808/FMS_01_20160808_001_005_mr_tfl_mpr_sag_p2_iso_1_0_freesurfer_swapdim highres_head
/usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard
did not find file: example_func2highres.mat. Generating transform.
/usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres --fmap=unwarp/FM_UD_fmap --fmapmag=unwarp/FM_UD_fmap_mag --fmapmagbrain=unwarp/FM_UD_fmap_mag_brain --echospacing=0.00037 --pedir=y-
Running FAST segmentation FLIRT pre-alignment Registering fieldmap to structural Running BBR with fieldmap 0.484845 0.999958 -0.008964 0.001863 0.000000 0.008968 0.999957 -0.002266 0.000000 -0.001843 0.002283 0.999996 0.000000 -1.269275 4.667767 7.217452 1.000000 Making warp fields and applying registration to EPI series
mv example_func2highres_fieldmap2str.mat unwarp/FM_UD_fmap_mag_brain2str.mat
mv example_func2highres_fieldmaprads2epi.mat unwarp/FM_UD_fmap2epi.mat
/usr/local/fsl/bin/immv example_func2highres_fieldmaprads2epi_shift unwarp/FM_UD_fmap2epi_shift
/usr/local/fsl/bin/immv example_func2highres_fieldmap2str unwarp/FM_UD_fmap_mag_brain2str
/usr/local/fsl/bin/fslstats FM_UD_fmap2epi_shift -R -P 1 -P 99
-6.508254 9.453788 -4.495969 4.562770
/usr/local/fsl/bin/flirt -ref ../example_func -in FM_UD_fmap_mag_brain -applyxfm -init FM_UD_fmap2epi.mat -out EF_UD_fmap_mag_brain
/usr/local/fsl/bin/fslmaths FM_UD_fmap2epi_shift -mul -1 grot
/usr/local/fsl/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift 0.0001 4.562770 grot 0.0001 4.49597 EF_UD_shift+mag
/usr/local/fsl/bin/slicer EF_UD_shift+mag -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_UD_shift+mag.png; rm sl?.png
/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif
/bin/cp /usr/local/fsl/etc/luts/ramp2.gif .ramp2.gif
overlay 0 0 FM_UD_fmap_mag_brain2str -a ../example_func2highres_fast_wmedge 0.001 5 fieldmap2edges
/usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png fieldmap2edges.png; rm sl?.png
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5175,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sh: line 1: 5175 Segmentation fault: 11 /usr/local/fsl/bin/slicer fieldmap2edges -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
Cannot open sla.png for reading
rm: sl?.png: No such file or directory
/usr/local/fsl/bin/slicer FM_UD_fmap_mag_brain2str ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str1.png ; /usr/local/fsl/bin/slicer ../highres FM_UD_fmap_mag_brain2str -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png FM_UD_fmap_mag_brain2str2.png ; /usr/local/fsl/bin/pngappend FM_UD_fmap_mag_brain2str1.png - FM_UD_fmap_mag_brain2str2.png FM_UD_fmap_mag_brain2str.png; /bin/rm -f sl?.png FM_UD_fmap_mag_brain2str2.png
/bin/rm FM_UD_fmap_mag_brain2str1.png
/usr/local/fsl/bin/flirt -ref ../highres -in ../example_func -out example_func_distorted2highres -applyxfm -init ../example_func2highres.mat -interp trilinear
/usr/local/fsl/bin/slicer example_func_distorted2highres ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func_distorted2highres1.png ; /usr/local/fsl/bin/slicer ../highres example_func_distorted2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func_distorted2highres2.png ; /usr/local/fsl/bin/pngappend example_func_distorted2highres1.png - example_func_distorted2highres2.png example_func_distorted2highres.png; /bin/rm -f sl?.png example_func_distorted2highres2.png
/bin/rm example_func_distorted2highres1.png
/usr/local/fsl/bin/slicer ../example_func2highres ../highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres1.png ; /usr/local/fsl/bin/slicer ../highres ../example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ../example_func2highres2.png ; /usr/local/fsl/bin/pngappend ../example_func2highres1.png - ../example_func2highres2.png ../example_func2highres.png; /bin/rm -f sl?.png ../example_func2highres2.png
/bin/rm ../example_func2highres1.png
/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat ../example_func2highres.mat
/usr/local/fsl/bin/applywarp -i ../example_func2highres -r ../example_func --premat=highres2example_func.mat -o example_func_undistorted
/usr/local/fsl/bin/overlay 0 0 example_func_distorted2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot
/usr/local/fsl/bin/slicer grot -c -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_D_edges.gif
slicer(5259,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5259,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5259,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sh: line 1: 5259 Segmentation fault: 11 /usr/local/fsl/bin/slicer grot -c -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
Cannot open sla.png for reading
/usr/local/fsl/bin/overlay 0 0 ../example_func2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot
/usr/local/fsl/bin/slicer grot -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png EF_U_edges.gif
slicer(5271,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5271,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
slicer(5271,0x7fffc12a13c0) malloc: *** mach_vm_map(size=18446744071830503424) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sh: line 1: 5271 Segmentation fault: 11 /usr/local/fsl/bin/slicer grot -s 3 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
Cannot open sla.png for reading
/usr/local/fsl/bin/whirlgif -o EF_UD_movie.gif -time 50 -loop 0 EF_D_edges.gif EF_U_edges.gif 2>&1; /bin/rm -f sla* slb* slc* sld* sle* slf* slg* slh* sli* slj* slk* sll* grot*
whirlgif Rev 3.04 (c) 1997-1999 by Hans Dinsen-Hansen (c) 1995-1996 by Kevin Kadow (c) 1990-1993 by Mark Podlipec Can't open EF_D_edges.gif for reading.
/usr/local/fsl/bin/imcp example_func_undistorted ../example_func
/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/local/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
/bin/rm example_func2highres1.png
did not find file: highres2standard.mat. Generating transform.
/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
/bin/rm highres2standard1.png
/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
/usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
Found file: example_func2standard.mat.
/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
/usr/local/fsl/bin/imcp ../example_func ../example_func_distorted
/usr/local/fsl/bin/imcp example_func ../example_func
Preprocessing:Stage 2
/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile reg/unwarp/EF_D_example_func -rmsrel -rmsabs -spline_final
/bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png
/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png
/usr/local/fsl/bin/applywarp -i reg/unwarp/FM_UD_fmap_mag_brain_mask -r example_func --rel --premat=reg/unwarp/FM_UD_fmap_mag_brain2str.mat --postmat=reg/highres2example_func.mat -o reg/unwarp/EF_UD_fmap_mag_brain_mask --paddingsize=1
cat mc/prefiltered_func_data_mcf.mat/MAT* > mc/prefiltered_func_data_mcf.cat
/usr/local/fsl/bin/applywarp -i prefiltered_func_data --premat=mc/prefiltered_func_data_mcf.cat -r example_func -o prefiltered_func_data_unwarp -w reg/example_func2highres_warp.nii.gz --postmat=reg/highres2example_func.mat --rel --interp=spline --paddingsize=1
/usr/local/fsl/bin/fslmaths prefiltered_func_data_unwarp -Tmean mean_func
/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv mask_mask mask
/usr/local/fsl/bin/fslmaths prefiltered_func_data_unwarp -mas mask prefiltered_func_data_bet
/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
0.000000 983.930908
/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 98.3930908 -Tmin -bin mask -odt char
/usr/local/fsl/bin/fslstats prefiltered_func_data_unwarp -k mask -p 50
701.136658
/usr/local/fsl/bin/fslmaths mask -dilF mask
/usr/local/fsl/bin/fslmaths prefiltered_func_data_unwarp -mas mask prefiltered_func_data_thresh
/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
/usr/local/fsl/bin/susan prefiltered_func_data_thresh 525.8524935 2.12314225053 3 1 1 mean_func 525.8524935 prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 14.26255479 prefiltered_func_data_intnorm
/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.5642023346 -1 -add tempMean prefiltered_func_data_tempfilt
/usr/local/fsl/bin/imrm tempMean
/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*
|