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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