No errors, but no file created. The following output: usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory and this is what I entered: file=c22061_MPRAGEreorient.nii absfile=`$FSLDIR/bin/fsl_abspath $file` cp ${absfile} test ks On Mon, Aug 6, 2018 at 9:23 AM, Matthew Webster < [log in to unmask]> wrote: > Hello Karen, > Can you try the following commands ( in the folder with > c22061_MPRAGEreorient_.nii ) > > file=c22061_MPRAGEreorient_.nii > absfile=`$FSLDIR/bin/fsl_abspath $file` > cp ${absfile} test > > And let me know if there are any errors ( and if test.nii.gz is created ). > > Kind Regards > Matthew > -------------------------------- > Dr Matthew Webster > FMRIB Centre > John Radcliffe Hospital > University of Oxford > > > On 6 Aug 2018, at 14:03, Karen Seymour <[log in to unmask]> wrote: > > > > Matthew, > > > > Just checking in about any thoughts for this problem..... > > > > Thanks! > > > > Karen > > > > On Fri, Aug 3, 2018 at 12:39 PM, Karen Seymour <[log in to unmask]> > wrote: > > Matthew, > > > > I actually deleted the files since I wasn't sure if they were "valid", > but saved a list of them: > > > > > > 2061_MB_run1CoregSource_fieldmap2str_init.mat > > 2061_MB_run1CoregSource_fieldmap2str.mat > > 2061_MB_run1CoregSource_fieldmap2str.nii.gz > > 2061_MB_run1CoregSource_fieldmaprads2str_dilated.nii.gz > > 2061_MB_run1CoregSource_fieldmaprads2str_pad0.nii.gz > > 2061_MB_run1CoregSource_fieldmaprads2str.nii.gz > > 2061_MB_run1CoregSource_init.mat > > > > On Fri, Aug 3, 2018 at 11:43 AM, Matthew Webster < > [log in to unmask]> wrote: > > Hi Karen, > > Thank you, it would be very useful to also know the exact filenames ( > e.g. obtained with ls in the folder containing > ra2061_MB_run1CoregSource.nii.gz ) to see how far epi_reg had progressed. > > > > Kind Regards > > Matthew > > -------------------------------- > > Dr Matthew Webster > > FMRIB Centre > > John Radcliffe Hospital > > University of Oxford > > > >> On 3 Aug 2018, at 15:56, Karen Seymour <[log in to unmask]> wrote: > >> > >> Sure, individual folders for each participant labelled with their > subject id. Within those folders are all the files being called by epi_reg. > I am using a bash script to batch epi_reg (see attached). I have a larger > script that does this for 2 runs and then applies the warps, but was > getting a lot of error messages so broke it down into smaller scripts. > >> > >> ks > >> > >> On Fri, Aug 3, 2018 at 10:50 AM, Matthew Webster < > [log in to unmask]> wrote: > >> Hi Karen, > >> Thank you - can you let me know the contents of the directory as well? > >> > >> Kind Regards > >> Matthew > >> -------------------------------- > >> Dr Matthew Webster > >> FMRIB Centre > >> John Radcliffe Hospital > >> University of Oxford > >> > >>> On 3 Aug 2018, at 15:11, Karen Seymour <[log in to unmask]> wrote: > >>> > >>> directory listing is: > >>> > >>> path=/Volumes/DCN_DATA$/fmri/UMD_collaboration/ADHD_BA_ > Study/Moneybags/Data_New > >>> > >>> DCN_DATA$ is a server > >>> > >>> I will try to run without the extension and let you know what happens > >>> > >>> ks > >>> > >>> On Fri, Aug 3, 2018 at 9:40 AM, Matthew Webster < > [log in to unmask]> wrote: > >>> Hello, > >>> Can you let me know the directory listing for the location where you > are running this? Also can you try rerunning with —out just set to > 2061_MB_run1CoregSource ( e.g. without extension ) and see if the error > messages change at all? > >>> > >>> Kind Regards > >>> Matthew > >>> -------------------------------- > >>> Dr Matthew Webster > >>> FMRIB Centre > >>> John Radcliffe Hospital > >>> University of Oxford > >>> > >>>> On 3 Aug 2018, at 14:22, Karen Seymour <[log in to unmask]> wrote: > >>>> > >>>> Hi all, > >>>> > >>>> I am using epi_reg to apply field maps to my EPI data, but keep > getting errors when I run the script. Here is the command I am running: > >>>> > >>>> epi_reg --epi=ra2061_MB_run1CoregSource.nii.gz > --t1=m2061_MPRAGEreorient.nii \ > >>>> --t1brain=2061_MPRAGEreorient_brain_4.nii.gz > --wmseg=c22061_MPRAGEreorient_.nii \ > >>>> --fmap=2061smoothfieldmapinRad.nii.gz --fmapmag=2061unwarped4DSEmean.nii.gz > --fmapmagbrain=2061unwarpedSEbrain.nii.gz \ > >>>> --echospacing=0.0007 --pedir=y --out=2061_MB_run1CoregSource.nii.gz > >>>> > >>>> Of note, the T1 (bias-corrected) and WM segmentation are from SPM. > >>>> > >>>> The error I keep getting is: > >>>> > >>>> Cannot open volume 2061_MB_run1CoregSource_fast_wmseg for reading! > >>>> > >>>> which is then followed by a whole set of errors about not being able > to open matrix files: > >>>> > >>>> Could not open matrix file 2061_MB_run1CoregSource.mat. > >>>> Cannot read input-matrix > >>>> Could not open matrix file 2061_MB_run1CoregSource_inv.mat > >>>> Cannot read concat-matrix > >>>> Could not open matrix file 2061_MB_run1CoregSource_ > fieldmaprads2epi.mat > >>>> > >>>> I assume all the errors are stemming from the first. > >>>> > >>>> Any help or advice would be greatly appreciated! > >>>> > >>>> Thanks > >>>> > >>>> Karen > >>>> > >>>> ############################################################ > ############ > >>>> > >>>> 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 > >> > >> > >> > >> To unsubscribe from the FSL list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > >> > >> <UMD_ADHD_BA_Epi_reg_run1.sh> > > > > > > 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