Hello Karen,
Can you also let me know what the results of running the two commands:
file=c22061_MPRAGEreorient_.nii
absfile=$FSLDIR/bin/fsl_abspath $file
Kind regards
Matthew
---------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 6 Aug 2018, at 14:46, Karen Seymour <[log in to unmask]> wrote:
>
> No errors, but no file created.
>
> The following output:
>
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
> cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
>
>
> and this is what I entered:
>
> file=c22061_MPRAGEreorient.nii absfile=`$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
> >>>>
> >>>> ########################################################################
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> >> <UMD_ADHD_BA_Epi_reg_run1.sh>
> >
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