 |
 |
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]<mailto:[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]<mailto:[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]<mailto:[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