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Subject:

fsl_anat unable to stat 'first_results.....no such file'

From:

Jennifer Vendemia <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 9 Oct 2015 03:31:24 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (13 lines) , fsl_anat_log.txt (274 lines)

When I run fsl_anat, it reports cp:cannot stat `first_results/T1_first_all_fast_firstseg.nii.gz': No such file or directory exists.'

However, when I look in the T1.anat directory is is clearly present, and I can locate it by inserting the full directory structure in front of /first_results.

I am using fsl installed on a small grid using  shared samba storage.  

I've tried running fsl from the users directory and the projects directory where I'm output files.  I've also tried running fsl_anat on the T1.anat directory and run into the same problem.  

I've attached a copy of the log file from one of my runs.





Script invoked from directory = /home/catdd_user Output directory = /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat Input image is /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1   /usr/local/fsl/bin/fslmaths T1 T1_orig /usr/local/fsl/bin/fslreorient2std T1 /usr/local/fsl/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std.mat /usr/local/fsl/bin/fslreorient2std T1 T1 /usr/local/fsl/bin/immv T1 T1_fullfov /usr/local/fsl/bin/robustfov -i T1_fullfov -r T1 -m T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_nonroi2roi.mat -inverse T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_orig2roi.mat -concat T1_nonroi2roi.mat T1_orig2std.mat /usr/local/fsl/bin/convert_xfm -omat T1_roi2orig.mat -inverse T1_orig2roi.mat /usr/local/fsl/bin/fslmaths T1 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1 -out T1_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1 -div T1_s20 T1_hpf /usr/local/fsl/bin/bet T1_hpf T1_hpf_brain -m -f 0.1 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -mas lesionmaskinv T1_hpf_brain_mask /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask T1_hpf_s20 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_s20 -out T1_hpf_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_brain_mask -out T1_initmask_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -div T1_initmask_s20 -mas T1_hpf_brain_mask T1_hpf2_s20 /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask -div T1_hpf2_s20 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -div 1.026896 -mul 276.000000 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -mas lesionmaskinv T1_hpf2_maskedbrain /usr/local/fsl/bin/fast -o T1_initfast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_hpf2_maskedbrain /usr/local/fsl/bin/fslmaths T1_initfast_restore -mas lesionmaskinv T1_initfast_maskedrestore /usr/local/fsl/bin/fast -o T1_initfast2 -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast_maskedrestore /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask T1_initfast2_brain_mask /usr/local/fsl/bin/fslmaths T1_initfast2_restore -mas lesionmaskinv T1_initfast2_maskedrestore /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast2_maskedrestore /usr/local/fsl/bin/fslmaths T1 -div T1_fast_restore -mas T1_initfast2_brain_mask T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_initfast2_brain_mask -ero -ero -ero -ero -mas lesionmaskinv T1_initfast2_brain_mask2 /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_initfast2_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1 -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/flirt -interp spline -dof 12 -in T1_biascorr -ref /usr/local/fsl/data/standard/MNI152_T1_2mm -dof 12 -omat T1_to_MNI_lin.mat -out T1_to_MNI_lin /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask -fillh -dilF MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/fnirt --in=T1_biascorr --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm --fout=T1_to_MNI_nonlin_field --jout=T1_to_MNI_nonlin_jac --iout=T1_to_MNI_nonlin --logout=T1_to_MNI_nonlin.txt --cout=T1_to_MNI_nonlin_coeff --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf --aff=T1_to_MNI_lin.mat --refmask=MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/invwarp --ref=T1_biascorr -w T1_to_MNI_nonlin_coeff -o MNI_to_T1_nonlin_field /usr/local/fsl/bin/applywarp --interp=nn --in=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask --ref=T1_biascorr -w MNI_to_T1_nonlin_field -o T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -fillh T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr -mas T1_biascorr_brain_mask T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain -mas lesionmaskinv T1_biascorr_maskedbrain /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 T1_biascorr_maskedbrain /usr/local/fsl/bin/immv T1_biascorr T1_biascorr_init /usr/local/fsl/bin/fslmaths T1_fast_restore T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -mas lesionmaskinv T1_biascorr_brain_mask2 /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_restore -mas T1_biascorr_brain_mask2 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_biascorr_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/applywarp -i T1_biascorr -w T1_to_MNI_nonlin_field -r /usr/local/fsl/data/standard/MNI152_T1_2mm -o T1_to_MNI_nonlin --interp=spline /usr/local/fsl/bin/bet T1_biascorr T1_biascorr_bet -s -m -f 0.1 /usr/local/fsl/bin/pairreg /usr/local/fsl/data/standard/MNI152_T1_2mm_brain T1_biascorr_bet /usr/local/fsl/data/standard/MNI152_T1_2mm_skull T1_biascorr_bet_skull T12std_skullcon.mat /usr/local/fsl/bin/first_flirt T1_biascorr T1_biascorr_to_std_sub mkdir first_results /usr/local/fsl/bin/run_first_all -i T1_biascorr -o first_results/T1_first -a T1_biascorr_to_std_sub.mat cp -r first_results/T1_first_all_fast_firstseg.nii.gz T1_subcort_seg.nii.gz Script invoked from directory = /home/catdd_user Output directory = /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat Input image is /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat/T1   /usr/local/fsl/bin/fslmaths T1 T1_orig /usr/local/fsl/bin/fslreorient2std T1 /usr/local/fsl/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std.mat /usr/local/fsl/bin/fslreorient2std T1 T1 /usr/local/fsl/bin/immv T1 T1_fullfov /usr/local/fsl/bin/robustfov -i T1_fullfov -r T1 -m T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_nonroi2roi.mat -inverse T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_orig2roi.mat -concat T1_nonroi2roi.mat T1_orig2std.mat /usr/local/fsl/bin/convert_xfm -omat T1_roi2orig.mat -inverse T1_orig2roi.mat /usr/local/fsl/bin/fslmaths T1 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1 -out T1_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1 -div T1_s20 T1_hpf /usr/local/fsl/bin/bet T1_hpf T1_hpf_brain -m -f 0.1 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -mas lesionmaskinv T1_hpf_brain_mask /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask T1_hpf_s20 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_s20 -out T1_hpf_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_brain_mask -out T1_initmask_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -div T1_initmask_s20 -mas T1_hpf_brain_mask T1_hpf2_s20 /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask -div T1_hpf2_s20 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -div 1.027368 -mul 279.000000 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -mas lesionmaskinv T1_hpf2_maskedbrain /usr/local/fsl/bin/fast -o T1_initfast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_hpf2_maskedbrain /usr/local/fsl/bin/fslmaths T1_initfast_restore -mas lesionmaskinv T1_initfast_maskedrestore /usr/local/fsl/bin/fast -o T1_initfast2 -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast_maskedrestore /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask T1_initfast2_brain_mask /usr/local/fsl/bin/fslmaths T1_initfast2_restore -mas lesionmaskinv T1_initfast2_maskedrestore /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast2_maskedrestore /usr/local/fsl/bin/fslmaths T1 -div T1_fast_restore -mas T1_initfast2_brain_mask T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_initfast2_brain_mask -ero -ero -ero -ero -mas lesionmaskinv T1_initfast2_brain_mask2 /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_initfast2_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1 -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/flirt -interp spline -dof 12 -in T1_biascorr -ref /usr/local/fsl/data/standard/MNI152_T1_2mm -dof 12 -omat T1_to_MNI_lin.mat -out T1_to_MNI_lin /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask -fillh -dilF MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/fnirt --in=T1_biascorr --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm --fout=T1_to_MNI_nonlin_field --jout=T1_to_MNI_nonlin_jac --iout=T1_to_MNI_nonlin --logout=T1_to_MNI_nonlin.txt --cout=T1_to_MNI_nonlin_coeff --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf --aff=T1_to_MNI_lin.mat --refmask=MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/invwarp --ref=T1_biascorr -w T1_to_MNI_nonlin_coeff -o MNI_to_T1_nonlin_field /usr/local/fsl/bin/applywarp --interp=nn --in=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask --ref=T1_biascorr -w MNI_to_T1_nonlin_field -o T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -fillh T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr -mas T1_biascorr_brain_mask T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain -mas lesionmaskinv T1_biascorr_maskedbrain /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 T1_biascorr_maskedbrain /usr/local/fsl/bin/immv T1_biascorr T1_biascorr_init /usr/local/fsl/bin/fslmaths T1_fast_restore T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -mas lesionmaskinv T1_biascorr_brain_mask2 /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_restore -mas T1_biascorr_brain_mask2 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_biascorr_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/applywarp -i T1_biascorr -w T1_to_MNI_nonlin_field -r /usr/local/fsl/data/standard/MNI152_T1_2mm -o T1_to_MNI_nonlin --interp=spline /usr/local/fsl/bin/bet T1_biascorr T1_biascorr_bet -s -m -f 0.1 /usr/local/fsl/bin/pairreg /usr/local/fsl/data/standard/MNI152_T1_2mm_brain T1_biascorr_bet /usr/local/fsl/data/standard/MNI152_T1_2mm_skull T1_biascorr_bet_skull T12std_skullcon.mat /usr/local/fsl/bin/first_flirt T1_biascorr T1_biascorr_to_std_sub mkdir first_results /usr/local/fsl/bin/run_first_all -i T1_biascorr -o first_results/T1_first -a T1_biascorr_to_std_sub.mat cp -r first_results/T1_first_all_fast_firstseg.nii.gz T1_subcort_seg.nii.gz Script invoked from directory = /home/catdd_user Output directory = /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat Input image is /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat/T1   /usr/local/fsl/bin/fslmaths T1 T1_orig /usr/local/fsl/bin/fslreorient2std T1 /usr/local/fsl/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std.mat /usr/local/fsl/bin/fslreorient2std T1 T1 /usr/local/fsl/bin/immv T1 T1_fullfov /usr/local/fsl/bin/robustfov -i T1_fullfov -r T1 -m T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_nonroi2roi.mat -inverse T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_orig2roi.mat -concat T1_nonroi2roi.mat T1_orig2std.mat /usr/local/fsl/bin/convert_xfm -omat T1_roi2orig.mat -inverse T1_orig2roi.mat /usr/local/fsl/bin/fslmaths T1 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1 -out T1_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1 -div T1_s20 T1_hpf /usr/local/fsl/bin/bet T1_hpf T1_hpf_brain -m -f 0.1 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -mas lesionmaskinv T1_hpf_brain_mask /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask T1_hpf_s20 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_s20 -out T1_hpf_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_brain_mask -out T1_initmask_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -div T1_initmask_s20 -mas T1_hpf_brain_mask T1_hpf2_s20 /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask -div T1_hpf2_s20 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -div 1.028617 -mul 275.000000 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -mas lesionmaskinv T1_hpf2_maskedbrain /usr/local/fsl/bin/fast -o T1_initfast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_hpf2_maskedbrain /usr/local/fsl/bin/fslmaths T1_initfast_restore -mas lesionmaskinv T1_initfast_maskedrestore /usr/local/fsl/bin/fast -o T1_initfast2 -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast_maskedrestore /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask T1_initfast2_brain_mask /usr/local/fsl/bin/fslmaths T1_initfast2_restore -mas lesionmaskinv T1_initfast2_maskedrestore /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast2_maskedrestore /usr/local/fsl/bin/fslmaths T1 -div T1_fast_restore -mas T1_initfast2_brain_mask T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_initfast2_brain_mask -ero -ero -ero -ero -mas lesionmaskinv T1_initfast2_brain_mask2 /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_initfast2_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1 -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/flirt -interp spline -dof 12 -in T1_biascorr -ref /usr/local/fsl/data/standard/MNI152_T1_2mm -dof 12 -omat T1_to_MNI_lin.mat -out T1_to_MNI_lin /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask -fillh -dilF MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/fnirt --in=T1_biascorr --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm --fout=T1_to_MNI_nonlin_field --jout=T1_to_MNI_nonlin_jac --iout=T1_to_MNI_nonlin --logout=T1_to_MNI_nonlin.txt --cout=T1_to_MNI_nonlin_coeff --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf --aff=T1_to_MNI_lin.mat --refmask=MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/invwarp --ref=T1_biascorr -w T1_to_MNI_nonlin_coeff -o MNI_to_T1_nonlin_field /usr/local/fsl/bin/applywarp --interp=nn --in=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask --ref=T1_biascorr -w MNI_to_T1_nonlin_field -o T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -fillh T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr -mas T1_biascorr_brain_mask T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain -mas lesionmaskinv T1_biascorr_maskedbrain /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 T1_biascorr_maskedbrain /usr/local/fsl/bin/immv T1_biascorr T1_biascorr_init /usr/local/fsl/bin/fslmaths T1_fast_restore T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -mas lesionmaskinv T1_biascorr_brain_mask2 /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_restore -mas T1_biascorr_brain_mask2 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_biascorr_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/applywarp -i T1_biascorr -w T1_to_MNI_nonlin_field -r /usr/local/fsl/data/standard/MNI152_T1_2mm -o T1_to_MNI_nonlin --interp=spline /usr/local/fsl/bin/bet T1_biascorr T1_biascorr_bet -s -m -f 0.1 /usr/local/fsl/bin/pairreg /usr/local/fsl/data/standard/MNI152_T1_2mm_brain T1_biascorr_bet /usr/local/fsl/data/standard/MNI152_T1_2mm_skull T1_biascorr_bet_skull T12std_skullcon.mat /usr/local/fsl/bin/first_flirt T1_biascorr T1_biascorr_to_std_sub mkdir first_results Script invoked from directory = /home/catdd_user Output directory = /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat Input image is /Volumes/catdd_projects/Ext_Collab/Paul_Beattie/1Qa_DryNeedlePneumoDeviceTest/MRI/individual_participants/Pneumo3Tests/T1.anat/T1   /usr/local/fsl/bin/fslmaths T1 T1_orig /usr/local/fsl/bin/fslreorient2std T1 /usr/local/fsl/bin/convert_xfm -omat T1_std2orig.mat -inverse T1_orig2std.mat /usr/local/fsl/bin/fslreorient2std T1 T1 /usr/local/fsl/bin/immv T1 T1_fullfov /usr/local/fsl/bin/robustfov -i T1_fullfov -r T1 -m T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_nonroi2roi.mat -inverse T1_roi2nonroi.mat /usr/local/fsl/bin/convert_xfm -omat T1_orig2roi.mat -concat T1_nonroi2roi.mat T1_orig2std.mat /usr/local/fsl/bin/convert_xfm -omat T1_roi2orig.mat -inverse T1_orig2roi.mat /usr/local/fsl/bin/fslmaths T1 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1 -out T1_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1 -div T1_s20 T1_hpf /usr/local/fsl/bin/bet T1_hpf T1_hpf_brain -m -f 0.1 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -mas lesionmaskinv T1_hpf_brain_mask /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask T1_hpf_s20 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_s20 -out T1_hpf_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask -subsamp2 -subsamp2 -subsamp2 -subsamp2 vol16 /usr/local/fsl/bin/flirt -in vol16 -ref T1_hpf_brain_mask -out T1_initmask_s20 -noresampblur -applyxfm -paddingsize 16 /usr/local/fsl/bin/imrm vol16 /usr/local/fsl/bin/fslmaths T1_hpf_s20 -div T1_initmask_s20 -mas T1_hpf_brain_mask T1_hpf2_s20 /usr/local/fsl/bin/fslmaths T1 -mas T1_hpf_brain_mask -div T1_hpf2_s20 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -div 1.027659 -mul 277.000000 T1_hpf2_brain /usr/local/fsl/bin/fslmaths T1_hpf2_brain -mas lesionmaskinv T1_hpf2_maskedbrain /usr/local/fsl/bin/fast -o T1_initfast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_hpf2_maskedbrain /usr/local/fsl/bin/fslmaths T1_initfast_restore -mas lesionmaskinv T1_initfast_maskedrestore /usr/local/fsl/bin/fast -o T1_initfast2 -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast_maskedrestore /usr/local/fsl/bin/fslmaths T1_hpf_brain_mask T1_initfast2_brain_mask /usr/local/fsl/bin/fslmaths T1_initfast2_restore -mas lesionmaskinv T1_initfast2_maskedrestore /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 --nopve --fixed=0 -v T1_initfast2_maskedrestore /usr/local/fsl/bin/fslmaths T1 -div T1_fast_restore -mas T1_initfast2_brain_mask T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_initfast2_brain_mask -ero -ero -ero -ero -mas lesionmaskinv T1_initfast2_brain_mask2 /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_initfast2_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1 -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/flirt -interp spline -dof 12 -in T1_biascorr -ref /usr/local/fsl/data/standard/MNI152_T1_2mm -dof 12 -omat T1_to_MNI_lin.mat -out T1_to_MNI_lin /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask -fillh -dilF MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/fnirt --in=T1_biascorr --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm --fout=T1_to_MNI_nonlin_field --jout=T1_to_MNI_nonlin_jac --iout=T1_to_MNI_nonlin --logout=T1_to_MNI_nonlin.txt --cout=T1_to_MNI_nonlin_coeff --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf --aff=T1_to_MNI_lin.mat --refmask=MNI152_T1_2mm_brain_mask_dil1 /usr/local/fsl/bin/invwarp --ref=T1_biascorr -w T1_to_MNI_nonlin_coeff -o MNI_to_T1_nonlin_field /usr/local/fsl/bin/applywarp --interp=nn --in=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask --ref=T1_biascorr -w MNI_to_T1_nonlin_field -o T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -fillh T1_biascorr_brain_mask /usr/local/fsl/bin/fslmaths T1_biascorr -mas T1_biascorr_brain_mask T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain -mas lesionmaskinv T1_biascorr_maskedbrain /usr/local/fsl/bin/fast -o T1_fast -l 10 -b -B -t 1 --iter=5 T1_biascorr_maskedbrain /usr/local/fsl/bin/immv T1_biascorr T1_biascorr_init /usr/local/fsl/bin/fslmaths T1_fast_restore T1_biascorr_brain /usr/local/fsl/bin/fslmaths T1_biascorr_brain_mask -mas lesionmaskinv T1_biascorr_brain_mask2 /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_restore -mas T1_biascorr_brain_mask2 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_fast_totbias -sub 1 T1_fast_totbias /usr/local/fsl/bin/fslsmoothfill -i T1_fast_totbias -m T1_biascorr_brain_mask2 -o T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_bias -add 1 T1_fast_bias /usr/local/fsl/bin/fslmaths T1_fast_totbias -add 1 T1_fast_totbias /usr/local/fsl/bin/fslmaths T1_biascorr_init -div T1_fast_bias T1_biascorr /usr/local/fsl/bin/applywarp -i T1_biascorr -w T1_to_MNI_nonlin_field -r /usr/local/fsl/data/standard/MNI152_T1_2mm -o T1_to_MNI_nonlin --interp=spline /usr/local/fsl/bin/bet T1_biascorr T1_biascorr_bet -s -m -f 0.1 /usr/local/fsl/bin/pairreg /usr/local/fsl/data/standard/MNI152_T1_2mm_brain T1_biascorr_bet /usr/local/fsl/data/standard/MNI152_T1_2mm_skull T1_biascorr_bet_skull T12std_skullcon.mat /usr/local/fsl/bin/first_flirt T1_biascorr T1_biascorr_to_std_sub mkdir first_results /usr/local/fsl/bin/run_first_all -i T1_biascorr -o first_results/T1_first -a T1_biascorr_to_std_sub.mat cp -r first_results/T1_first_all_fast_firstseg.nii.gz T1_subcort_seg.nii.gz

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