Hi Sarah,
You might not have permission to write to the output directory. Can you run this command in a terminal:
chmod -R u+rwx /Users/schiang/fsl_course_data/
and then try re-running BET?
Paul
On Jan 3 2020, at 1:17 pm, Sarah <[log in to unmask]> wrote:
> Hello,
>
> I am attempting to follow the FSL course and continue to run into a problem while running BET, whether from the GUI or the command line. I am using macOS Catalina 10.15.2. The error message when running BET and the report output are below. Thank you so much in advance, and my apologies if the solution is simple!
> Sarahs-MacBook-Pro-2:subj1_preproc schiang$ Fsl_gui
> /usr/local/fsl/bin/bet /Users/schiang/fsl_course_data/intro/structural /Users/schiang/fsl_course_data/intro/structural_brain -f 0.5 -g 0
> Error. Expected to find bet2 output (/Users/schiang/fsl_course_data/intro/structural_brain), but it did not exist. Perhaps this is a writing issue or memory issue
> libc++abi.dylib: terminating with uncaught exception of type NiftiIO::NiftiException: Error: cant open file /Users/schiang/fsl_course_data/intro/structural_brain.nii.gz
> /usr/local/fsl/bin/bet: line 393: 28802 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
> Finished
>
>
> Sarahs-MacBook-Pro-2:subj1_preproc schiang$ fslerrorreport
> /usr/local/fsl/bin/fslerrorreport: line 101: vmstat: command not found
> Image Exception : #63 :: No image files match: /Users/schiang/fsl_course_data/fdt1/subj1_preproc
> No image files match: /Users/schiang/fsl_course_data/fdt1/subj1_preproc
>
> ######################################################################
> #### MACHINE INFORMATION
> ######################################################################
>
> Uname:
> Darwin
>
> df:
> Filesystem 512-blocks Used Available Capacity iused ifree %iused Mounted on
> /dev/disk1s1 489825072 395387296 67249704 86% 1636564 2447488796 0% /System/Volumes/Data
>
> quota:
> Disk quotas for user schiang (uid 501): none
>
> Memory and Swap info:
> Mach Virtual Memory Statistics: (page size of 4096 bytes)
> Pages free: 119351.
> Pages active: 1527325.
> Pages inactive: 1456460.
> Pages speculative: 70825.
> Pages throttled: 0.
> Pages wired down: 640287.
> Pages purgeable: 42296.
> "Translation faults": 1493201970.
> Pages copy-on-write: 17538774.
> Pages zero filled: 377589430.
> Pages reactivated: 2139446.
> Pages purged: 6968567.
> File-backed pages: 777297.
> Anonymous pages: 2277313.
> Pages stored in compressor: 1005198.
> Pages occupied by compressor: 379585.
> Decompressions: 4590818.
> Compressions: 6845157.
> Pageins: 12307068.
> Pageouts: 37675.
> Swapins: 4867134.
> Swapouts: 5010533.
>
> ######################################################################
> #### ENVIRONMENT INFORMATION
> ######################################################################
>
> FSLMULTIFILEQUIT=TRUE
> FSLGECUDAQ=cuda.q
> FSLTCLSH=/usr/local/fsl/bin/fsltclsh
> FSLMACHINELIST=
> FSLREMOTECALL=
> FSLWISH=/usr/local/fsl/bin/fslwish
> FSLDIR=/usr/local/fsl
> FSLLOCKDIR=
> FSLOUTPUTTYPE=NIFTI_GZ
>
> PATH=/usr/local/fsl/bin:/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
> ######################################################################
> #### DIRECTORY INFORMATION
> ######################################################################
>
> PWD:
> /Users/schiang/fsl_course_data/fdt1/subj1_preproc
>
> total 557288
> dr-xr-xr-x 11 schiang staff 352 Jul 21 2017 .
> dr-xr-xr-x 5 schiang staff 160 Jul 21 2017 ..
> -r-xr-xr-x 1 schiang staff 8196 Jul 21 2017 .DS_Store
> -r-xr-xr-x 1 schiang staff 25 Jul 21 2017 acqparams.txt
> -r-xr-xr-x 1 schiang staff 82040617 Jul 21 2017 b1500.nii.gz
> -r-xr-xr-x 1 schiang staff 542 Jul 21 2017 bvals
> -r-xr-xr-x 1 schiang staff 6407 Jul 21 2017 bvecs
> -r-xr-xr-x 1 schiang staff 197392512 Jul 21 2017 dwidata.nii.gz
> -r-xr-xr-x@ 1 schiang staff 230 Jul 21 2017 index.txt
> -r-xr-xr-x 1 schiang staff 1811770 Jul 21 2017 nodif_PA.nii.gz
> dr-xr-xr-x 10 schiang staff 320 Jul 21 2017 pre_baked
>
> ######################################################################
> #### IMAGE INFORMATION
> ######################################################################
>
>
> This error report is saved in the file: /tmp/fsl_5lUPNj.gz
> ########################################################################
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