JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives

FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font
LISTSERV Archives

LISTSERV Archives
FSL Home

FSL Home
FSL October 2015

FSL October 2015

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

 Log In

Log In

 Get Password

Get Password

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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2024
April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager