Hello Karen,
Odd - it looks like python thinks the directory has been deleted ( also it looks like the directory is called “2016 cnir_ra”, which could cause problems with other tools due to the space in the name ). Can you check that the directory still exists ( e.g. by cd-ing up and down )? If the directory does still exist, then as a temporary fix you could try replacing the lines in $FSLDIR/bin/epi_reg reading:
absfile=`$FSLDIR/bin/fsl_abspath $file`
With
absfile=$file
and try the epi_reg call again
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 7 Aug 2018, at 15:09, Karen Seymour <[log in to unmask]> wrote:
>
> Traceback (most recent call last):
> File "/usr/local/fsl/bin/fsl_abspath", line 70, in <module>
> print (os.path.realpath(sys.argv[1]))
> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 376, in realpath
> return abspath(path)
> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py", line 364, in abspath
> cwd = os.getcwd()
> OSError: [Errno 2] No such file or directory
> CRC-3-MACPRO:2061 cnir_ra$
> CRC-3-MACPRO:2061 cnir_ra$
>
>
> On Tue, Aug 7, 2018 at 6:01 AM, Matthew Webster <[log in to unmask]> wrote:
> Hello Karen,
> I took the underscored version of the name from the command line call in your first email, but if it’s a typo please ignore it. Can you try the following commands and let me know the full output in the terminal:
>
> $FSLDIR/bin/fsl_abspath c22061_MPRAGEreorient.nii
> file=c22061_MPRAGEreorient.nii
> absfile=$FSLDIR/bin/fsl_abspath $file
> echo $absfile
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> > On 6 Aug 2018, at 17:45, Karen Seymour <[log in to unmask]> wrote:
> >
> > I think the answer was 2061.
> >
> > One question in the command file=c22061_MPRAGEreorient_.nii the file name is incorrect- it should be just c22061_MPRAGEreorient.nii (without the underscore before .nii) Was that just a typo by you or do you want me to include that underscore?
> >
> > ks
> >
> > On Mon, Aug 6, 2018 at 12:05 PM, Matthew Webster <[log in to unmask]> wrote:
> > Hello Karen,
> > Can you also let me know what the results of running the two commands:
> >
> > file=c22061_MPRAGEreorient_.nii
> > absfile=$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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> > > >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
> > > >>>
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> > > >>
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> > > >>
> > > >> <UMD_ADHD_BA_Epi_reg_run1.sh>
> > > >
> > > >
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> > >
> > > ########################################################################
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