Hi,
I don't really understand why reorienting could cause a problem unless something is failing in the process somewhere. It isn't something that we've seen before. However, it could also be just that the generation of the webpage images is failing. This is what Matthew was trying to figure out - and for that we'll need to have access to the original images. I think that his email to you accidentally put a colon ":" at the end of the link. So try copying the link text and then deleting this final character. Hopefully that will solve the problem.
All the best,
Mark
> On 6 Jan 2018, at 12:38, Susanne Becker <[log in to unmask]> wrote:
>
> Hi Mark,
>
> thanks a lot!
>
> When I try to run with B0 field unwrapping, I get an error message an some parts of the unwrapping are not executed. Before applying the field map, I prepared the field map using the command fsl_prepare_fieldmap (it is SIEMENS data). The structural image a get form the scanner is wrongly oriented, which I reorint using the fslreorient2std command. The resulting pictures of th prepared field map and the reoriented structural look find.
> When using Feat, I get the following error message (Below I attached the whole resulting log in the html-report).
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63126 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63128 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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: cannot remove 'sl?.png': No such file or directory
>
>
> Although the error message above shows fsl 5.0.9, I'm actually using the latest version of FSL. I copied this log from an analysis I tried on my laptop, with fsl 5.0.9. But the error message looks exactly the same on my work computer with fsl 5.0.10.
>
> Since I expected this to be a RAM problem, I tried this feat on different computers/servers including a high performance computing cluster. Even when using this cluster, I ended up with the same error message.
> Here is a list of things I also tried to solve this or at least get an idea what is causing the problem:
> - doing the same analysis with a different subject with equivalent data
> - applying the command fslreorient2std also to the field map and/or the epi
> - using the command fslswapdim instead of fslreorient2std for the structural and/or the field map and/or the epi
> - double-checking the preparation of the field map
>
> What works
> - running feat without unwrapping
> - running feat with unwrapping but not reorienting the structural
> The latter point is what confuses me. If the structural is not reoriented it works perfectly well and running the analysis is also rather fast. This is why expected that somehow reorienting the structural is the problem. As mentioned above, we tried different options using differnt ways to reorient only the structural or all fills need. When checking the orientations in the header for the structural, the field map, and the epi these are all the same and correct after reorienting the structural.
>
> I response to Matthew answer a few mintues are yours, I wanted to upload the files he requested, but the link seem not working.
> All the best
> Susanne
>
>
> Feat main script
>
>
> /bin/cp /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/design.fsf design.fsf
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat_model design
>
> mkdir .files;cp /opt/bwhpc/common/bio/fsl/5.0.9/doc/fsl.css .files;cp -r /opt/bwhpc/common/bio/fsl/5.0.9/doc/images .files/images
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fsl_sub -T 10 -l logs -N feat0_init /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/design.fsf -D /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -I 1 -init
> 60591
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fsl_sub -T 246 -l logs -N feat2_pre -j 60591 /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/design.fsf -D /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -I 1 -prestats
> 60758
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fsl_sub -T 44 -l logs -N feat3_film -j 60758 /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/design.fsf -D /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -I 1 -stats
> 64817
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fsl_sub -T 119 -l logs -N feat4_post -j 64817 /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/design.fsf -D /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -poststats 0
> 65029
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 60758,64817,65029 /opt/bwhpc/common/bio/fsl/5.0.9/bin/feat /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/design.fsf -D /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -stop
>
> Initialisation
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_002_mr_ep2d_96x96_32Channel_painreward_20160808/FMS_01_20160808_001_002_mr_ep2d_96x96_32Channel_painreward prefiltered_func_data -odt float
> Total original volumes = 460
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslroi prefiltered_func_data example_func 230 1
>
> Preprocessing:Stage 1
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/mainfeatreg -F 6.00 -d /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat -l /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/logs/feat2_pre -R /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/report_unwarp.html -r /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/report_reg.html -i /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/example_func.nii.gz -h /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/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_brain -w BBR -x 90 -s /pfs/data1/software_uc1/bwhpc/common/bio/fsl/5.0.9/data/standard/MNI152lin_T1_2mm_brain -y 6 -z 90 -a /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_rads -b /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_mag_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 "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat"
> Option -l ( logfile )input with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/logs/feat2_pre"
> Option -R ( html unwarping report ) selected with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/report_unwarp.html"
> Option -r ( html registration report ) selected with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/report_reg.html"
> Option -i ( main input ) input with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/example_func.nii.gz"
> Option -h ( high-res structural image ) selected with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/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_brain"
> Option -w ( highres dof ) selected with argument "BBR"
> Option -x ( highres search ) selected with argument "90"
> Option -s ( standard image ) selected with argument "/pfs/data1/software_uc1/bwhpc/common/bio/fsl/5.0.9/data/standard/MNI152lin_T1_2mm_brain"
> Option -y ( standard dof ) selected with argument "6"
> Option -z ( standard search ) selected with argument "90"
> Option -a ( fieldmap image ) selected with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_rads"
> Option -b ( field ) selected with argument "/pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_mag_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 /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/test+++.feat/reg
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths ../example_func EF_D_example_func
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_rads FM_UD_fmap
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_mag_brain FM_UD_fmap_mag_brain
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/FMS_01/1_003_gre_field_mapping_20160808/FMS_01_20160808_001_003_gre_field_mapping_01_fieldmap_mag_brain FM_UD_fmap_mag
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap_mag_brain -V | awk '{ print $1 }'
> 127247
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print $1 }'
> 470016
> 0.270729
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_mag_brain -bin FM_UD_fmap_mag_brain_mask -odt short
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/cluster -i FM_UD_fmap_mag_brain_mask_inv -t 0.5 --no_table -o FM_UD_fmap_mag_brain_mask_idx
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap_mag_brain_mask_idx -R | awk '{ print $2 }'
> 230.000000
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
> 0.623596
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap -sub 0.623596 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap_mag_brain -P 98
> 993.038452
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_mag_brain -thr 496.519 -bin FM_UD_fmap_mag_brain_mask50
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_mag_brain -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap_mag_brain
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_mag_brain_mask -ero FM_UD_fmap_mag_brain_mask_ero
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fugue --loadfmap=FM_UD_fmap --savefmap=FM_UD_fmap_tmp_fmapfilt --mask=FM_UD_fmap_mag_brain_mask --despike --despikethreshold=2.1
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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*
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap -k FM_UD_fmap_mag_brain_mask -P 50
> -0.623596
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap -sub -0.623596 -mas FM_UD_fmap_mag_brain_mask FM_UD_fmap
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap -R | awk '{ print $1 }'
> -1196.628906
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap -sub -1196.628906 -add 10 -mas FM_UD_fmap_mag_brain_mask grot
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats grot -l 1 -p 0.1 -p 95
> 331.761719 1455.432861
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 0 0 FM_UD_fmap_mag -a grot 331.761719 1455.432861 fmap+mag
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/sigloss -i FM_UD_fmap --te=0.03 -m FM_UD_fmap_mag_brain_mask -s FM_UD_fmap_sigloss
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_sigloss -mul FM_UD_fmap_mag_brain FM_UD_fmap_mag_brain_siglossed -odt float
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap_sigloss -thr 0.9 FM_UD_fmap_sigloss -odt float
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 1 0 FM_UD_fmap_mag_brain -a FM_UD_fmap_sigloss 0 1 FM_UD_sigloss+mag
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/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_brain highres
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data2/home/hd/hd_hd/hd_bm132/Dokumente/test_EVA/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 highres_head
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths /pfs/data1/software_uc1/bwhpc/common/bio/fsl/5.0.9/data/standard/MNI152lin_T1_2mm_brain standard
>
> did not find file: example_func2highres.mat. Generating transform.
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 0.486215 0.999961 -0.008737 0.001502 0.000000 0.008740 0.999960 -0.002032 0.000000 -0.001484 0.002045 0.999997 0.000000 -1.346998 4.745049 7.260902 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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/immv example_func2highres_fieldmaprads2epi_shift unwarp/FM_UD_fmap2epi_shift
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/immv example_func2highres_fieldmap2str unwarp/FM_UD_fmap_mag_brain2str
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats FM_UD_fmap2epi_shift -R -P 1 -P 99
> -6.000514 9.290301 -2.590751 2.464431
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/flirt -ref ../example_func -in FM_UD_fmap_mag_brain -applyxfm -init FM_UD_fmap2epi.mat -out EF_UD_fmap_mag_brain
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths FM_UD_fmap2epi_shift -mul -1 grot
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 1 0 EF_UD_fmap_mag_brain -a FM_UD_fmap2epi_shift 0.0001 2.464431 grot 0.0001 2.59075 EF_UD_shift+mag
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 /opt/bwhpc/common/bio/fsl/5.0.9/etc/luts/ramp.gif .ramp.gif
>
>
> /bin/cp /opt/bwhpc/common/bio/fsl/5.0.9/etc/luts/ramp2.gif .ramp2.gif
>
>
> overlay 0 0 FM_UD_fmap_mag_brain2str -a ../example_func2highres_fast_wmedge 0.001 5 fieldmap2edges
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63126 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63128 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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: cannot remove 'sl?.png': No such file or directory
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/flirt -ref ../highres -in ../example_func -out example_func_distorted2highres -applyxfm -init ../example_func2highres.mat -interp trilinear
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/bin/pngappend ../example_func2highres1.png - ../example_func2highres2.png ../example_func2highres.png; /bin/rm -f sl?.png ../example_func2highres2.png
>
>
> /bin/rm ../example_func2highres1.png
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/convert_xfm -inverse -omat highres2example_func.mat ../example_func2highres.mat
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/applywarp -i ../example_func2highres -r ../example_func --premat=highres2example_func.mat -o example_func_undistorted
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 0 0 example_func_distorted2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63297 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63298 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 0 0 ../example_func2highres -a ../example_func2highres_fast_wmedge 0.001 10 grot
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63307 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
> sh: line 1: 63308 Segmentation fault /opt/bwhpc/common/bio/fsl/5.0.9/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
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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.
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/imcp example_func_undistorted ../example_func
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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.
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
>
>
> /bin/rm highres2standard1.png
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
>
> Found file: example_func2standard.mat.
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/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 ; /opt/bwhpc/common/bio/fsl/5.0.9/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/imcp ../example_func ../example_func_distorted
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/imcp example_func ../example_func
>
> Preprocessing:Stage 2
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/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
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_unwarp -Tmean mean_func
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/bet2 mean_func mask -f 0.3 -n -m; /opt/bwhpc/common/bio/fsl/5.0.9/bin/immv mask_mask mask
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_unwarp -mas mask prefiltered_func_data_bet
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
> 0.000000 981.008057
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_bet -thr 98.1008057 -Tmin -bin mask -odt char
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats prefiltered_func_data_unwarp -k mask -p 50
> 700.218262
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths mask -dilF mask
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_unwarp -mas mask prefiltered_func_data_thresh
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/susan prefiltered_func_data_thresh 525.1636965 2.12314225053 3 1 1 mean_func 525.1636965 prefiltered_func_data_smooth
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_smooth -mul 14.2812613476 prefiltered_func_data_intnorm
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.5642023346 -1 -add tempMean prefiltered_func_data_tempfilt
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/imrm tempMean
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths filtered_func_data -Tmean mean_func
>
> /bin/rm -rf prefiltered_func_data*
>
> Stats
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con
> Log directory is: stats
> paradigm.getDesignMatrix().Nrows()=460
> paradigm.getDesignMatrix().Ncols()=2
> sizeTS=460
> numTS=140010
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 9666.8
> sig = 1596
> Spatially smoothing auto corr estimates
> ....................
> Completed
> Tukey M = 21
> Tukey estimates... Completed
> Completed
> Prewhitening and Computing PEs...
> Percentage done:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
> Saving results...
> Completed
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/smoothest -d 458 -m mask -r stats/res4d > stats/smoothness
>
> Post-stats
>
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
>
> echo 140010 > thresh_zstat1.vol
> zstat1: DLH=0.282083 VOLUME=140010 RESELS=16.374
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.282083 --volume=140010 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/cluster2html . cluster_zstat1
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.282083 --volume=140010 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/cluster2html . cluster_zstat1 -std
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null
> 2.300581 4.383682
> Rendering using zmin=2.300581 zmax=4.383682
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/overlay 1 0 example_func -a thresh_zstat1 2.300581 4.383682 rendered_thresh_zstat1
>
> /opt/bwhpc/common/bio/fsl/5.0.9/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png
>
> /bin/cp /opt/bwhpc/common/bio/fsl/5.0.9/etc/luts/ramp.gif .ramp.gif
>
> mkdir -p tsplot ; /opt/bwhpc/common/bio/fsl/5.0.9/bin/tsplot . -f filtered_func_data -o tsplot
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