JISCMail - FSL Archives

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.

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