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Hi, Matthew (and FSL support team),

Any further updates on what might have gone wrong with my analysis?

Kind regards,
Jake

On Tue, Jun 9, 2020 at 10:53 PM Jake Rambirgton <[log in to unmask]>
wrote:

> Sure, here it is.
>
> *</pre><hr>Preprocessing:Stage 1<br><pre>*
>
>
>
> * /usr/local/fsl/bin/mainfeatreg -F 6.00 -d  /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica  -l  /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica /logs/feat2_pre -R
>  /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica
> /report_unwarp.html -r  /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica /report_reg.html  -i
>  /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica
> /example_func.nii.gz  -n 10 -h / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain.nii.gz -w  BBR -x 90 -s
>  /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 -a /
> /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fieldmap/fieldmap_fout_to_T1_brain_rad.nii.gz -b /
> /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain.nii.gz
> -e 39 -f 10 -g 0.26 -p y- -w BBR*
>
> *Option -F ( FEAT version parameter ) selected with  argument "6.00"*
>
> *Option -d ( output directory ) selected with  argument "
> /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica "*
>
> *Option -l ( logfile )input with argument " /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica /logs/feat2_pre"*
>
> *Option -R ( html unwarping report ) selected with  argument "
> /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica
> /report_unwarp.html"*
>
> *Option -r ( html registration report ) selected with  argument "
> /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica
> /report_reg.html"*
>
> *Option -i ( main input ) input with argument " /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica /example_func.nii.gz"*
>
> *Option -n ( use nonlinear reg ) input with argument "10"*
>
> *Option -h ( high-res structural image ) selected with  argument "/
> /usr/local/fsl/bin/feat /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain.nii.gz"*
>
> *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 "/
> /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fieldmap/fieldmap_fout_to_T1_brain_rad.nii.gz"*
>
> *Option -b ( field ) selected with  argument "/ /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain.nii.gz"*
>
> *Option -e ( echo time ) selected with  argument "39"*
>
> *Option -f ( signal loss Threshold ) selected with  argument "10"*
>
> *Option -g ( echo spacing ) selected with  argument "0.26"*
>
> *Option -p ( phase encoding direction ) selected with  argument "y-"*
>
> *Option -w ( highres dof ) selected with  argument "BBR"*
>
> *</pre><hr>Registration<br><pre>*
>
>
>
> */bin/mkdir -p  /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/rfMRI.ica /reg*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths ../example_func EF_D_example_func*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fieldmap/fieldmap_fout_to_T1_brain_rad.nii.gz
> FM_UD_fmap*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain FM_UD_fmap_mag_brain*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1.nii.gz  FM_UD_fmap_mag*
>
>
>
>
>
> * /usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -V | awk '{ print $1 }'*
>
> *1721505*
>
>
>
> * /usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -v | awk '{ print $1 }'*
>
> *9586980*
>
> *0.179567*
>
>
>
> * /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 }'*
>
> *8.000000*
>
>
>
> * /usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain_mask_idx -thr 8.000000
> -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*
>
> *-35.167191*
>
>
>
> * /usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -35.167191 -mas
> FM_UD_fmap_mag_brain_mask FM_UD_fmap*
>
>
>
>
>
> * /usr/local/fsl/bin/fslstats FM_UD_fmap_mag_brain -P 98*
>
> *490.000000*
>
>
>
> * /usr/local/fsl/bin/fslmaths FM_UD_fmap_mag_brain -thr 245 -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*
>
> *-1.796761*
>
>
>
> * /usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -1.796761 -mas
> FM_UD_fmap_mag_brain_mask FM_UD_fmap*
>
>
>
>
>
> * /usr/local/fsl/bin/fslstats FM_UD_fmap -R | awk '{ print $1 }'*
>
> *-669.776794*
>
>
>
> * /usr/local/fsl/bin/fslmaths FM_UD_fmap -sub -669.776794 -add 10 -mas
> FM_UD_fmap_mag_brain_mask grot*
>
>
>
>
>
> * /usr/local/fsl/bin/fslstats grot -l 1 -p 0.1 -p 95*
>
> *169.342590 826.463562*
>
>
>
> * /usr/local/fsl/bin/overlay 0 0 FM_UD_fmap_mag -a grot 169.342590
> 826.463562 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=0.039 -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 / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain highres*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1.nii.gz  highres_head*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain_wmseg highres_wmseg*
>
>
>
> *Checking for / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain_warp and /
> /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain.mat*
>
>
>
> * /usr/local/fsl/bin/fslmaths / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain_warp
> highres2standard_warp*
>
>
>
>
>
> *cp / /usr/local/fsl/bin/feat
> /mnt/d/MRI/Data/P002/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain.mat
> highres2standard.mat*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths
>  /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths  /usr/local/fsl/data/standard/MNI152_T1_2mm
> standard_head*
>
>
>
>
>
> * /usr/local/fsl/bin/fslmaths
>  /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil standard_mask*
>
>
>
> *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=0.00026 --pedir=y-*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *FLIRT pre-alignment Registering fieldmap to structural Running BBR with
> fieldmap 0.674834 0.999724 0.022670 0.006116 0.000000 -0.022706 0.999724
> 0.006003 0.000000 -0.005978 -0.006140 0.999963 0.000000 3.311896 -0.353082
> 1.934221 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*
>
> *-2.419019 3.440551 -1.604954 1.302772*
>
>
>
> * /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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> * /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 1.302772 grot 0.0001 1.60495 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*
>
>
>
>
>
> * /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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> */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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> */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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> * /usr/local/fsl/bin/overlay  0 0 example_func_distorted2highres -a
> ../example_func2highres_fast_wmedge 0.001 10 grot*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> * /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*
>
>
>
>
>
> * /usr/local/fsl/bin/overlay  0 0 ../example_func2highres -a
> ../example_func2highres_fast_wmedge 0.001 10 grot*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> * /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*
>
>
>
>
>
> * /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 Processed 2 files.*
>
>
>
> * /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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> */bin/rm example_func2highres1.png*
>
>
>
>
>
> * /usr/local/fsl/bin/applywarp --ref=standard --in=highres
> --out=highres2standard --warp=highres2standard_warp*
>
>
>
>
>
> * /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/convertwarp --ref=standard
> --premat=example_func2highres.mat --warp1=highres2standard_warp
> --out=example_func2standard_warp*
>
>
>
>
>
> * /usr/local/fsl/bin/applywarp --ref=standard --in=example_func
> --out=example_func2standard --warp=example_func2standard_warp*
>
>
>
>
>
> * /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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
>
>
> * /usr/local/fsl/bin/imcp ../example_func ../example_func_distorted*
>
>
>
>
>
> * /usr/local/fsl/bin/imcp example_func ../example_func*
>
>
>
> *</pre><hr>Preprocessing:Stage 2<br><pre>*
>
>
>
> * /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*
>
> *Warning: An input intended to be a single 3D volume has multiple
> timepoints. Input will be truncated to first volume, but this functionality
> is deprecated and will be removed in a future release.*
>
>
>
> */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*
>
> On Tue, Jun 9, 2020 at 8:04 PM Matthew Webster <
> [log in to unmask]> wrote:
>
>> Hi Jake,
>> Can you let me know the contents of the “plain” feat2_pre file too?
>>
>> Kind Regards
>> Matthew
>> --------------------------------
>> Dr Matthew Webster
>> FMRIB Centre
>> John Radcliffe Hospital
>> University of Oxford
>>
>> On 9 Jun 2020, at 17:30, Jake Rambirgton <[log in to unmask]>
>> wrote:
>>
>> Hi Matthew,
>>
>> Here are all the files in logs
>> feat0  feat1  feat1a_init  feat1a_init.e33106  feat1a_init.o33106
>>  feat2_pre  feat2_pre.e33222  feat2_pre.o33222  feat9
>>
>> *feat2_pre.e33222: *
>> can't read "relrms": no such variable
>>     while executing
>> "if { [ catch {
>>
>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>     switch -- [ lindex $argv $argindex ] {
>>
>>         -I {
>>             incr arginde..."
>>     (file "/opt/fmrib/fsl/bin/feat" line 312)
>>
>> *feat2_pre.o33222*:
>> "Error encountered while running in main feat script, halting.
>> can't read "relrms": no such variable"
>>
>> *feat1a_init.e33106* is empty
>>
>> Kind regards,
>> Jake
>>
>> On Tue, Jun 9, 2020 at 3:20 PM Matthew Webster <
>> [log in to unmask]> wrote:
>>
>>> Hi Jake,
>>> Just to confirm are all those logs completely empty?
>>>
>>> Kind Regards
>>> Matthew
>>> --------------------------------
>>> Dr Matthew Webster
>>> FMRIB Centre
>>> John Radcliffe Hospital
>>> University of Oxford
>>>
>>> On 9 Jun 2020, at 14:31, Jake Rambirgton <[log in to unmask]>
>>> wrote:
>>>
>>> Hi Matthew,
>>>
>>> I have checked. There are no further feat2_pre* messages there.
>>>
>>> Jake.
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>
>>
>> ------------------------------
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>>
>>
>> ------------------------------
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>

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